IBAMR config failure

94 views
Skip to first unread message

jmda...@vcu.edu

unread,
Mar 9, 2018, 5:12:33 PM3/9/18
to IBAMR Users
It errors finding libpetsc. 

It was created by IBAMR configure 171104, which was

generated by GNU Autoconf 2.69.  Invocation command line was


  $ ./configure CC=mpicc CXX=mpicxx --with-hypre=/gpfs_fs/home/rasegal/software/hypre BOOST_ROOT=/gpfs_fs/home/rasegal/softw

are/boost_1_66_0 PETSC_DIR=/gpfs_fs/home/rasegal/software/petsc PETSC_ARCH=arch-linux2-c-debug


## --------- ##

## Platform. ##

## --------- ##


hostname = godel21

uname -m = x86_64

uname -r = 2.6.32-696.3.2.el6.x86_64

uname -s = Linux

uname -v = #1 SMP Tue Jun 20 01:26:55 UTC 2017


/usr/bin/uname -p = unknown

/bin/uname -X     = unknown


/bin/arch              = x86_64

/usr/bin/arch -k       = unknown

/usr/convex/getsysinfo = unknown

/usr/bin/hostinfo      = unknown

/bin/machine           = unknown

/usr/bin/oslevel       = unknown

/bin/universe          = unknown


PATH: /usr/global/sge/bin/lx24-amd64

PATH: /usr/global/R-2.13.1/bin

PATH: /usr/lib64/qt-3.3/bin

PATH: /usr/global/jre/bin

PATH: /usr/global/454/bin

PATH: /usr/local/bin

PATH: /bin

PATH: /usr/bin

PATH: /usr/local/sbin

PATH: /usr/sbin

PATH: /sbin

PATH: /gpfs_fs/home/rasegal/bin

PATH: /usr/mpi/gcc/openmpi-1.10.4/bin

PATH: /usr/mpi/gcc/openmpi-1.10.4/lib64

PATH: /usr/mpi/gcc/openmpi-1.10.4/include



## ----------- ##

## Core tests. ##

## ----------- ##


configure:2787: checking for a BSD-compatible install

configure:2855: result: /usr/bin/install -c

configure:2866: checking whether build environment is sane

configure:2921: result: yes

configure:3072: checking for a thread-safe mkdir -p

configure:3111: result: /bin/mkdir -p

configure:3118: checking for gawk

configure:3134: found /bin/gawk

configure:3145: result: gawk

configure:3156: checking whether make sets $(MAKE)

configure:3178: result: yes

configure:3207: checking whether make supports nested variables

configure:3224: result: yes

configure:3361: checking whether make supports nested variables

configure:3378: result: yes

configure:3390: checking whether to enable maintainer-specific portions of Makefiles

configure:3399: result: no

configure:3473: checking for gcc

configure:3500: result: mpicc

configure:3729: checking for C compiler version

configure:3738: mpicc --version >&5

gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)

Copyright (C) 2010 Free Software Foundation, Inc.

This is free software; see the source for copying conditions.  There is NO

warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.


configure:3749: $? = 0

configure:3738: mpicc -v >&5

Using built-in specs.

Target: x86_64-redhat-linux

Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.

redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib -

-enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-languages=c,c++,objc,obj-c++,java,fo

rtran,ada --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-mult

ifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --w

ith-cloog --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux

Thread model: posix

gcc version 4.4.7 20120313 (Red Hat 4.4.7-18) (GCC) 

configure:3749: $? = 0

configure:3738: mpicc -V >&5

gcc: '-V' option must have argument

configure:3749: $? = 1

configure:3738: mpicc -qversion >&5

gcc: unrecognized option '-qversion'

gcc: no input files

configure:3749: $? = 1

configure:3769: checking whether the C compiler works

configure:3791: mpicc  -I/gpfs_fs/home/rasegal/software/petsc/include  conftest.c  >&5

configure:3795: $? = 0

configure:3843: result: yes

configure:3846: checking for C compiler default output file name

configure:3848: result: a.out

configure:3854: checking for suffix of executables

configure:3861: mpicc -o conftest  -I/gpfs_fs/home/rasegal/software/petsc/include  conftest.c  >&5

configure:3865: $? = 0

configure:3887: result: 

configure:3909: checking whether we are cross compiling

configure:3917: mpicc -o conftest  -I/gpfs_fs/home/rasegal/software/petsc/include  conftest.c  >&5

configure:3921: $? = 0

configure:3928: ./conftest

configure:3932: $? = 0

configure:3947: result: no

configure:3952: checking for suffix of object files

configure:3974: mpicc -c  -I/gpfs_fs/home/rasegal/software/petsc/include conftest.c >&5

configure:3978: $? = 0

configure:3999: result: o

configure:4003: checking whether we are using the GNU C compiler

configure:4022: mpicc -c  -I/gpfs_fs/home/rasegal/software/petsc/include conftest.c >&5

configure:4022: $? = 0

configure:4031: result: yes

configure:4040: checking whether mpicc accepts -g

configure:4060: mpicc -c -g -I/gpfs_fs/home/rasegal/software/petsc/include conftest.c >&5

configure:4060: $? = 0

configure:4101: result: yes

configure:4118: checking for mpicc option to accept ISO C89

configure:4181: mpicc  -c -g -O2 -I/gpfs_fs/home/rasegal/software/petsc/include conftest.c >&5

configure:4181: $? = 0

configure:4194: result: none needed

configure:4219: checking whether mpicc understands -c and -o together

configure:4241: mpicc -c conftest.c -o conftest2.o

configure:4244: $? = 0

configure:4241: mpicc -c conftest.c -o conftest2.o

configure:4244: $? = 0

configure:4256: result: yes

configure:4284: checking for style of include used by make

configure:4312: result: GNU

configure:4338: checking dependency style of mpicc

configure:4449: result: gcc3

configure:4469: checking how to run the C preprocessor

configure:4500: mpicc -E -I/gpfs_fs/home/rasegal/software/petsc/include conftest.c

configure:4500: $? = 0

configure:4514: mpicc -E -I/gpfs_fs/home/rasegal/software/petsc/include conftest.c

conftest.c:11:28: error: ac_nonexistent.h: No such file or directory

configure:4514: $? = 1

configure: failed program was:

| /* confdefs.h */

| #define PACKAGE_NAME "IBAMR"

| #define PACKAGE_TARNAME "IBAMR"

| #define PACKAGE_VERSION "171104"

| #define PACKAGE_STRING "IBAMR 171104"

| #define PACKAGE_BUGREPORT "boy...@gmail.com"

| #define PACKAGE_URL "https://ibamr.github.io"

| #define PACKAGE "IBAMR"

| #define VERSION "171104"

| /* end confdefs.h.  */

| #include <ac_nonexistent.h>

configure:4539: result: mpicc -E

configure:4559: mpicc -E -I/gpfs_fs/home/rasegal/software/petsc/include conftest.c

configure:4559: $? = 0

configure:4573: mpicc -E -I/gpfs_fs/home/rasegal/software/petsc/include conftest.c

conftest.c:11:28: error: ac_nonexistent.h: No such file or directory

configure:4573: $? = 1

configure: failed program was:

| /* confdefs.h */

| #define PACKAGE_NAME "IBAMR"

| #define PACKAGE_TARNAME "IBAMR"

| #define PACKAGE_VERSION "171104"

| #define PACKAGE_STRING "IBAMR 171104"

| #define PACKAGE_BUGREPORT "boy...@gmail.com"

| #define PACKAGE_URL "https://ibamr.github.io"

| #define PACKAGE "IBAMR"

| #define VERSION "171104"

| /* end confdefs.h.  */

| #include <ac_nonexistent.h>

configure:4713: checking for C++ compiler version

configure:4722: mpicxx --version >&5

g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)

Copyright (C) 2010 Free Software Foundation, Inc.

This is free software; see the source for copying conditions.  There is NO

warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.


configure:4733: $? = 0

configure:4722: mpicxx -v >&5

Using built-in specs.

Target: x86_64-redhat-linux

Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.

redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib -

-enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-languages=c,c++,objc,obj-c++,java,fo

rtran,ada --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-mult

ifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --w

ith-cloog --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux

Thread model: posix

gcc version 4.4.7 20120313 (Red Hat 4.4.7-18) (GCC) 

configure:4733: $? = 0

configure:4722: mpicxx -V >&5

g++: '-V' option must have argument

configure:4733: $? = 1

configure:4722: mpicxx -qversion >&5

g++: unrecognized option '-qversion'

g++: no input files

configure:4733: $? = 1

configure:4737: checking whether we are using the GNU C++ compiler

configure:4756: mpicxx -c  -I/gpfs_fs/home/rasegal/software/petsc/include conftest.cpp >&5

configure:4756: $? = 0

configure:4765: result: yes

configure:4774: checking whether mpicxx accepts -g

configure:4794: mpicxx -c -g -I/gpfs_fs/home/rasegal/software/petsc/include conftest.cpp >&5

configure:4794: $? = 0

configure:4835: result: yes

configure:4860: checking dependency style of mpicxx

configure:4971: result: gcc3

configure:4991: checking how to run the C++ preprocessor

configure:5018: mpicxx -E -I/gpfs_fs/home/rasegal/software/petsc/include conftest.cpp

configure:5018: $? = 0

configure:5032: mpicxx -E -I/gpfs_fs/home/rasegal/software/petsc/include conftest.cpp

conftest.cpp:11:28: error: ac_nonexistent.h: No such file or directory

configure:5032: $? = 1

configure: failed program was:

| /* confdefs.h */

| #define PACKAGE_NAME "IBAMR"

| #define PACKAGE_TARNAME "IBAMR"

| #define PACKAGE_VERSION "171104"

| #define PACKAGE_STRING "IBAMR 171104"

| #define PACKAGE_BUGREPORT "boy...@gmail.com"

| #define PACKAGE_URL "https://ibamr.github.io"

| #define PACKAGE "IBAMR"

| #define VERSION "171104"

| /* end confdefs.h.  */

| #include <ac_nonexistent.h>

configure:5057: result: mpicxx -E

configure:5077: mpicxx -E -I/gpfs_fs/home/rasegal/software/petsc/include conftest.cpp

configure:5077: $? = 0

configure:5091: mpicxx -E -I/gpfs_fs/home/rasegal/software/petsc/include conftest.cpp

conftest.cpp:11:28: error: ac_nonexistent.h: No such file or directory

configure:5091: $? = 1

configure: failed program was:

| /* confdefs.h */

| #define PACKAGE_NAME "IBAMR"

| #define PACKAGE_TARNAME "IBAMR"

| #define PACKAGE_VERSION "171104"

| #define PACKAGE_STRING "IBAMR 171104"

| #define PACKAGE_BUGREPORT "boy...@gmail.com"

| #define PACKAGE_URL "https://ibamr.github.io"

| #define PACKAGE "IBAMR"

| #define VERSION "171104"

| /* end confdefs.h.  */

| #include <ac_nonexistent.h>

configure:5172: checking for gfortran

configure:5188: found /usr/bin/gfortran

configure:5199: result: gfortran

configure:5225: checking for Fortran compiler version

configure:5234: gfortran --version >&5

GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)

Copyright (C) 2010 Free Software Foundation, Inc.


GNU Fortran comes with NO WARRANTY, to the extent permitted by law.

You may redistribute copies of GNU Fortran

under the terms of the GNU General Public License.

For more information about these matters, see the file named COPYING


configure:5245: $? = 0

configure:5234: gfortran -v >&5

Using built-in specs.

Target: x86_64-redhat-linux

Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.

redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib -

-enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-languages=c,c++,objc,obj-c++,java,fo

rtran,ada --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-mult

ifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --w

ith-cloog --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux

Thread model: posix

gcc version 4.4.7 20120313 (Red Hat 4.4.7-18) (GCC) 

configure:5245: $? = 0

configure:5234: gfortran -V >&5

gfortran: '-V' option must have argument

configure:5245: $? = 1

configure:5234: gfortran -qversion >&5

gfortran: unrecognized option '-qversion'

gfortran: no input files

configure:5245: $? = 1

configure:5254: checking whether we are using the GNU Fortran compiler

configure:5267: gfortran -c   conftest.F >&5

configure:5267: $? = 0

configure:5276: result: yes

configure:5282: checking whether gfortran accepts -g

configure:5293: gfortran -c -g  conftest.f >&5

configure:5293: $? = 0

configure:5301: result: yes

configure:5334: checking build system type

configure:5348: result: x86_64-pc-linux-gnu

configure:5368: checking host system type

configure:5381: result: x86_64-pc-linux-gnu

configure:5406: checking how to get verbose linking output from gfortran

configure:5416: gfortran -c -g -O2  conftest.f >&5

configure:5416: $? = 0

configure:5434: gfortran -o conftest -g -O2 -v conftest.f

Using built-in specs.

Target: x86_64-redhat-linux

Thread model: posix

gcc version 4.4.7 20120313 (Red Hat 4.4.7-18) (GCC) 

 /usr/libexec/gcc/x86_64-redhat-linux/4.4.7/f951 conftest.f -ffixed-form -quiet -dumpbase conftest.f -mtune=generic -auxbase

 conftest -g -O2 -version -fintrinsic-modules-path /usr/lib/gcc/x86_64-redhat-linux/4.4.7/finclude -o /tmp/ccKwJ67U.s

GNU Fortran (GCC) version 4.4.7 20120313 (Red Hat 4.4.7-18) (x86_64-redhat-linux)

compiled by GNU C version 4.4.7 20120313 (Red Hat 4.4.7-18), GMP version 4.3.1, MPFR version 2.4.1.

GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072

 as -V -Qy -o /tmp/cc88RIYF.o /tmp/ccKwJ67U.s

GNU assembler version 2.20.51.0.2 (x86_64-redhat-linux) using BFD version version 2.20.51.0.2-5.47.el6_9.1 20100205

 /usr/libexec/gcc/x86_64-redhat-linux/4.4.7/collect2 --eh-frame-hdr --build-id -m elf_x86_64 --hash-style=gnu -dynamic-linke

r /lib64/ld-linux-x86-64.so.2 -o conftest /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crt1.o /usr/lib/gcc/x86_6

4-redhat-linux/4.4.7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/4.4.7/crtbegin.o -L/usr/lib/gcc/x86_64-redhat

-linux/4.4.7 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64 -L/lib/../l

ib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../.. /tmp/cc88RIYF.o -lgfortranbegin -lgfortran -lm -l

gcc_s -lgcc -lc -lgcc_s -lgcc /usr/lib/gcc/x86_64-redhat-linux/4.4.7/crtend.o /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../.

./../lib64/crtn.o

configure:5517: result: -v

configure:5519: checking for Fortran libraries of gfortran

configure:5542: gfortran -o conftest -g -O2 -v conftest.f

Using built-in specs.

Target: x86_64-redhat-linux

Thread model: posix

gcc version 4.4.7 20120313 (Red Hat 4.4.7-18) (GCC) 

 /usr/libexec/gcc/x86_64-redhat-linux/4.4.7/f951 conftest.f -ffixed-form -quiet -dumpbase conftest.f -mtune=generic -auxbase

 conftest -g -O2 -version -fintrinsic-modules-path /usr/lib/gcc/x86_64-redhat-linux/4.4.7/finclude -o /tmp/ccv88pR0.s

GNU Fortran (GCC) version 4.4.7 20120313 (Red Hat 4.4.7-18) (x86_64-redhat-linux)

compiled by GNU C version 4.4.7 20120313 (Red Hat 4.4.7-18), GMP version 4.3.1, MPFR version 2.4.1.

GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072

 as -V -Qy -o /tmp/cc5TFrRL.o /tmp/ccv88pR0.s

GNU assembler version 2.20.51.0.2 (x86_64-redhat-linux) using BFD version version 2.20.51.0.2-5.47.el6_9.1 20100205

 /usr/libexec/gcc/x86_64-redhat-linux/4.4.7/collect2 --eh-frame-hdr --build-id -m elf_x86_64 --hash-style=gnu -dynamic-linke

r /lib64/ld-linux-x86-64.so.2 -o conftest /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crt1.o /usr/lib/gcc/x86_6

4-redhat-linux/4.4.7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/4.4.7/crtbegin.o -L/usr/lib/gcc/x86_64-redhat

-linux/4.4.7 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64 -L/lib/../l

ib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../.. /tmp/cc5TFrRL.o -lgfortranbegin -lgfortran -lm -l

gcc_s -lgcc -lc -lgcc_s -lgcc /usr/lib/gcc/x86_64-redhat-linux/4.4.7/crtend.o /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../.

./../lib64/crtn.o

configure:5738: result:  -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64

 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../.. -lgfortranbegin -lgfortran -lm

configure:5755: checking for dummy main to link with Fortran libraries

configure:5789: mpicc -o conftest -g -O2 -I/gpfs_fs/home/rasegal/software/petsc/include  conftest.c   -L/usr/lib/gcc/x86_64-

redhat-linux/4.4.7 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib

/gcc/x86_64-redhat-linux/4.4.7/../../.. -lgfortranbegin -lgfortran -lm >&5

configure:5789: $? = 0

configure:5834: result: none

configure:5867: checking for Fortran name-mangling scheme

configure:5880: gfortran -c -g -O2  conftest.f >&5

configure:5880: $? = 0

configure:5921: mpicc -o conftest -g -O2 -I/gpfs_fs/home/rasegal/software/petsc/include  conftest.c cfortran_test.o   -L/usr

/lib/gcc/x86_64-redhat-linux/4.4.7 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../

lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../.. -lgfortranbegin -lgfortran -lm >&5

/tmp/ccdcesn0.o: In function `main':

/gpfs_fs/home/rasegal/software/IBAMR/conftest.c:30: undefined reference to `foobar'

collect2: ld returned 1 exit status

configure:5921: $? = 1

configure: failed program was:

| /* confdefs.h */

| #define PACKAGE_NAME "IBAMR"

| #define PACKAGE_TARNAME "IBAMR"

| #define PACKAGE_VERSION "171104"

| #define PACKAGE_STRING "IBAMR 171104"

| #define PACKAGE_BUGREPORT "boy...@gmail.com"

| #define PACKAGE_URL "https://ibamr.github.io"

| #define PACKAGE "IBAMR"

| #define VERSION "171104"

| /* end confdefs.h.  */

| 

| /* Override any GCC internal prototype to avoid an error.

|    Use char because int might match the return type of a GCC

|    builtin and then its argument prototype would still apply.  */

| #ifdef __cplusplus

| extern "C"

| #endif

| char foobar ();

| #ifdef FC_DUMMY_MAIN

| #ifndef FC_DUMMY_MAIN_EQ_F77

| #  ifdef __cplusplus

|      extern "C"

| #  endif

|    int FC_DUMMY_MAIN() { return 1; }

| #endif

| #endif

| int

| main ()

| {

| return foobar ();

|   ;

|   return 0;

| }

configure:5921: mpicc -o conftest -g -O2 -I/gpfs_fs/home/rasegal/software/petsc/include  conftest.c cfortran_test.o   -L/usr

/lib/gcc/x86_64-redhat-linux/4.4.7 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../

lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../.. -lgfortranbegin -lgfortran -lm >&5

configure:5921: $? = 0

configure:5979: mpicc -o conftest -g -O2 -I/gpfs_fs/home/rasegal/software/petsc/include  conftest.c cfortran_test.o   -L/usr

/lib/gcc/x86_64-redhat-linux/4.4.7 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../

lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../.. -lgfortranbegin -lgfortran -lm >&5

configure:5979: $? = 0

configure:6021: result: lower case, underscore, no extra underscore

configure:6094: checking for Fortran flag to compile .f files

configure:6114: gfortran -c -g -O2  conftest.f >&5

configure:6114: $? = 0

configure:6123: result: none

configure:6305: checking for gcc

configure:6332: result: mpicc

configure:6561: checking for C compiler version

configure:6570: mpicc --version >&5

gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)

Copyright (C) 2010 Free Software Foundation, Inc.

This is free software; see the source for copying conditions.  There is NO

warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.


configure:6581: $? = 0

configure:6570: mpicc -v >&5

Using built-in specs.

Target: x86_64-redhat-linux

Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.

redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib -

-enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-languages=c,c++,objc,obj-c++,java,fo

rtran,ada --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-mult

ifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --w

ith-cloog --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux

Thread model: posix

gcc version 4.4.7 20120313 (Red Hat 4.4.7-18) (GCC) 

configure:6581: $? = 0

configure:6570: mpicc -V >&5

gcc: '-V' option must have argument

configure:6581: $? = 1

configure:6570: mpicc -qversion >&5

gcc: unrecognized option '-qversion'

gcc: no input files

configure:6581: $? = 1

configure:6585: checking whether we are using the GNU C compiler

configure:6621: result: yes

configure:6630: checking whether mpicc accepts -g

configure:6715: result: yes

configure:6732: checking for mpicc option to accept ISO C89

configure:6816: result: none needed

configure:6841: checking whether mpicc understands -c and -o together

configure:6886: result: yes

configure:6905: checking dependency style of mpicc

configure:7016: result: gcc3

configure:7057: checking for function MPI_Init

configure:7090: mpicc -o conftest -g -O2 -I/gpfs_fs/home/rasegal/software/petsc/include  conftest.c  >&5

configure:7090: $? = 0

configure:7097: result: yes

configure:7108: checking for mpi.h

configure:7129: mpicc -c -g -O2 -I/gpfs_fs/home/rasegal/software/petsc/include conftest.c >&5

configure:7129: $? = 0

configure:7130: result: yes

configure:7387: checking for C++ compiler version

configure:7396: mpicxx --version >&5

g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)

Copyright (C) 2010 Free Software Foundation, Inc.

This is free software; see the source for copying conditions.  There is NO

warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.


configure:7407: $? = 0

configure:7396: mpicxx -v >&5

Using built-in specs.

Target: x86_64-redhat-linux

Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.

redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib -

-enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-languages=c,c++,objc,obj-c++,java,fo

rtran,ada --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-mult

ifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --w

ith-cloog --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux

Thread model: posix

gcc version 4.4.7 20120313 (Red Hat 4.4.7-18) (GCC) 

configure:7407: $? = 0

configure:7396: mpicxx -V >&5

g++: '-V' option must have argument

configure:7407: $? = 1

configure:7396: mpicxx -qversion >&5

g++: unrecognized option '-qversion'

g++: no input files

configure:7407: $? = 1

configure:7411: checking whether we are using the GNU C++ compiler

configure:7447: result: yes

configure:7456: checking whether mpicxx accepts -g

configure:7541: result: yes

configure:7566: checking dependency style of mpicxx

configure:7677: result: gcc3

configure:7720: checking for function MPI_Init

configure:7749: mpicxx -o conftest -g -O2 -I/gpfs_fs/home/rasegal/software/petsc/include  conftest.cpp  >&5

configure:7749: $? = 0

configure:7756: result: yes

configure:7767: checking for mpi.h

configure:7788: mpicxx -c -g -O2 -I/gpfs_fs/home/rasegal/software/petsc/include conftest.cpp >&5

configure:7788: $? = 0

configure:7789: result: yes

configure:7826: checking for grep that handles long lines and -e

configure:7884: result: /bin/grep

configure:7889: checking for egrep

configure:7951: result: /bin/grep -E

configure:7956: checking for ANSI C header files

configure:7984: mpicxx -c -g -O2 -I/gpfs_fs/home/rasegal/software/petsc/include conftest.cpp >&5

configure:7984: $? = 0

configure:8057: mpicxx -o conftest -g -O2 -I/gpfs_fs/home/rasegal/software/petsc/include  conftest.cpp  >&5

configure:8057: $? = 0

configure:8057: ./conftest

configure:8057: $? = 0

configure:8068: result: yes

configure:8081: checking for sys/types.h

configure:8081: mpicxx -c -g -O2 -I/gpfs_fs/home/rasegal/software/petsc/include conftest.cpp >&5

configure:8081: $? = 0

configure:8081: result: yes

configure:8081: checking for sys/stat.h

configure:8081: mpicxx -c -g -O2 -I/gpfs_fs/home/rasegal/software/petsc/include conftest.cpp >&5

configure:8081: $? = 0

configure:8081: result: yes

configure:8081: checking for stdlib.h

configure:8081: mpicxx -c -g -O2 -I/gpfs_fs/home/rasegal/software/petsc/include conftest.cpp >&5

configure:8081: $? = 0

configure:8081: result: yes

configure:8081: checking for string.h

configure:8081: mpicxx -c -g -O2 -I/gpfs_fs/home/rasegal/software/petsc/include conftest.cpp >&5

configure:8081: $? = 0

configure:8081: result: yes

configure:8081: checking for memory.h

configure:8081: mpicxx -c -g -O2 -I/gpfs_fs/home/rasegal/software/petsc/include conftest.cpp >&5

configure:8081: $? = 0

configure:8081: result: yes

configure:8081: checking for strings.h

configure:8081: mpicxx -c -g -O2 -I/gpfs_fs/home/rasegal/software/petsc/include conftest.cpp >&5

configure:8081: $? = 0

configure:8081: result: yes

configure:8081: checking for inttypes.h

configure:8081: mpicxx -c -g -O2 -I/gpfs_fs/home/rasegal/software/petsc/include conftest.cpp >&5

configure:8081: $? = 0

configure:8081: result: yes

configure:8081: checking for stdint.h

configure:8081: mpicxx -c -g -O2 -I/gpfs_fs/home/rasegal/software/petsc/include conftest.cpp >&5

configure:8081: $? = 0

configure:8081: result: yes

configure:8081: checking for unistd.h

configure:8081: mpicxx -c -g -O2 -I/gpfs_fs/home/rasegal/software/petsc/include conftest.cpp >&5

configure:8081: $? = 0

configure:8081: result: yes

configure:8093: checking whether sys/types.h defines makedev

configure:8117: mpicxx -o conftest -g -O2 -I/gpfs_fs/home/rasegal/software/petsc/include  conftest.cpp  >&5

configure:8117: $? = 0

configure:8126: result: yes

configure:8151: checking for ANSI C header files

configure:8263: result: yes

configure:8317: checking how to print strings

configure:8344: result: printf

configure:8365: checking for a sed that does not truncate output

configure:8429: result: /bin/sed

configure:8447: checking for fgrep

configure:8509: result: /bin/grep -F

configure:8544: checking for ld used by mpicc

configure:8611: result: /usr/bin/ld

configure:8618: checking if the linker (/usr/bin/ld) is GNU ld

configure:8633: result: yes

configure:8645: checking for BSD- or MS-compatible name lister (nm)

configure:8699: result: /usr/bin/nm -B

configure:8829: checking the name lister (/usr/bin/nm -B) interface

configure:8836: mpicxx -c -g -O2 -I/gpfs_fs/home/rasegal/software/petsc/include conftest.cpp >&5

configure:8839: /usr/bin/nm -B "conftest.o"

configure:8842: output

0000000000000000 B some_variable

configure:8849: result: BSD nm

configure:8852: checking whether ln -s works

configure:8856: result: yes

configure:8864: checking the maximum length of command line arguments

configure:8995: result: 1966080

configure:9043: checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format

configure:9083: result: func_convert_file_noop

configure:9090: checking how to convert x86_64-pc-linux-gnu file names to toolchain format

configure:9110: result: func_convert_file_noop

configure:9117: checking for /usr/bin/ld option to reload object files

configure:9124: result: -r

configure:9198: checking for objdump

configure:9214: found /usr/bin/objdump

configure:9225: result: objdump

configure:9257: checking how to recognize dependent libraries

configure:9457: result: pass_all

configure:9542: checking for dlltool

configure:9572: result: no

configure:9602: checking how to associate runtime and link libraries

configure:9629: result: printf %s\n

configure:9689: checking for ar

configure:9705: found /usr/bin/ar

configure:9716: result: ar

configure:9753: checking for archiver @FILE support

configure:9778: mpicxx -c -g -O2 -I/gpfs_fs/home/rasegal/software/petsc/include conftest.cpp >&5

configure:9778: $? = 0

configure:9781: ar cru libconftest.a @conftest.lst >&5

configure:9784: $? = 0

configure:9789: ar cru libconftest.a @conftest.lst >&5

ar: conftest.o: No such file or directory

configure:9792: $? = 1

configure:9804: result: @

configure:9862: checking for strip

configure:9878: found /usr/bin/strip

configure:9889: result: strip

configure:9961: checking for ranlib

configure:9977: found /usr/bin/ranlib

configure:9988: result: ranlib

configure:10090: checking command to parse /usr/bin/nm -B output from mpicc object

configure:10243: mpicxx -c -g -O2 -I/gpfs_fs/home/rasegal/software/petsc/include conftest.cpp >&5

configure:10246: $? = 0

configure:10250: /usr/bin/nm -B conftest.o \| sed -n -e 's/^.*[ ]\([ABCDGIRSTW][ABCDGIRSTW]*\)[ ][ ]*\([_A-Za-z][_A-Za-z0-9]

*\)$/\1 \2 \2/p' | sed '/ __gnu_lto/d' \> conftest.nm

configure:10253: $? = 0

configure:10319: mpicxx -o conftest -g -O2 -I/gpfs_fs/home/rasegal/software/petsc/include  conftest.cpp conftstm.o >&5

configure:10322: $? = 0

configure:10360: result: ok

configure:10407: checking for sysroot

configure:10437: result: no

configure:10444: checking for a working dd

configure:10482: result: /bin/dd

configure:10486: checking how to truncate binary pipes

configure:10501: result: /bin/dd bs=4096 count=1

configure:10637: mpicxx -c -g -O2 -I/gpfs_fs/home/rasegal/software/petsc/include conftest.cpp >&5

configure:10640: $? = 0

configure:10838: checking for mt

configure:10868: result: no

configure:10888: checking if : is a manifest tool

configure:10894: : '-?'

configure:10902: result: no

configure:11584: checking for dlfcn.h

configure:11584: mpicxx -c -g -O2 -I/gpfs_fs/home/rasegal/software/petsc/include conftest.cpp >&5

configure:11584: $? = 0

configure:11584: result: yes

configure:11850: checking for objdir

configure:11865: result: .libs

configure:12129: checking if mpicc supports -fno-rtti -fno-exceptions

configure:12147: mpicc -c -g -O2 -I/gpfs_fs/home/rasegal/software/petsc/include -fno-rtti -fno-exceptions conftest.c >&5

cc1: warning: command line option "-fno-rtti" is valid for C++/ObjC++ but not for C

configure:12151: $? = 0

configure:12164: result: no

configure:12522: checking for mpicc option to produce PIC

configure:12529: result: -fPIC -DPIC

configure:12537: checking if mpicc PIC flag -fPIC -DPIC works

configure:12555: mpicc -c -g -O2 -I/gpfs_fs/home/rasegal/software/petsc/include -fPIC -DPIC -DPIC conftest.c >&5

configure:12559: $? = 0

configure:12572: result: yes

configure:12601: checking if mpicc static flag -static works

configure:12629: result: no

configure:12644: checking if mpicc supports -c -o file.o

configure:12665: mpicc -c -g -O2 -I/gpfs_fs/home/rasegal/software/petsc/include -o out/conftest2.o conftest.c >&5

configure:12669: $? = 0

configure:12691: result: yes

configure:12699: checking if mpicc supports -c -o file.o

configure:12746: result: yes

configure:12779: checking whether the mpicc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries

configure:14054: result: yes

configure:14091: checking whether -lc should be explicitly linked in

configure:14099: mpicc -c -g -O2 -I/gpfs_fs/home/rasegal/software/petsc/include conftest.c >&5

configure:14102: $? = 0

configure:14117: mpicc -shared  -fPIC -DPIC conftest.o  -v -Wl,-soname -Wl,conftest -o conftest 2\>\&1 \| /bin/grep  -lc  \>

/dev/null 2\>\&1

configure:14120: $? = 0

configure:14134: result: no

configure:14294: checking dynamic linker characteristics

configure:14883: mpicc -o conftest -g -O2 -I/gpfs_fs/home/rasegal/software/petsc/include  -Wl,-rpath -Wl,/foo conftest.c  >&

5

configure:14883: $? = 0

configure:15120: result: GNU/Linux ld.so

configure:15242: checking how to hardcode library paths into programs

configure:15267: result: immediate

configure:15855: checking whether stripping libraries is possible

configure:15860: result: yes

configure:15895: checking if libtool supports shared libraries

configure:15897: result: yes

configure:15900: checking whether to build shared libraries

configure:15925: result: yes

configure:15928: checking whether to build static libraries

configure:15932: result: yes

configure:15955: checking how to run the C++ preprocessor

configure:16021: result: mpicxx -E

configure:16041: mpicxx -E -I/gpfs_fs/home/rasegal/software/petsc/include conftest.cpp

configure:16041: $? = 0

configure:16055: mpicxx -E -I/gpfs_fs/home/rasegal/software/petsc/include conftest.cpp

conftest.cpp:28:28: error: ac_nonexistent.h: No such file or directory

configure:16055: $? = 1

configure: failed program was:

| /* confdefs.h */

| #define PACKAGE_NAME "IBAMR"

| #define PACKAGE_TARNAME "IBAMR"

| #define PACKAGE_VERSION "171104"

| #define PACKAGE_STRING "IBAMR 171104"

| #define PACKAGE_BUGREPORT "boy...@gmail.com"

| #define PACKAGE_URL "https://ibamr.github.io"

| #define PACKAGE "IBAMR"

| #define VERSION "171104"

| #define FC_FUNC(name,NAME) name ## _

| #define FC_FUNC_(name,NAME) name ## _

| #define HAVE_MPI 1

| #define HAVE_MPI 1

| #define STDC_HEADERS 1

| #define HAVE_SYS_TYPES_H 1

| #define HAVE_SYS_STAT_H 1

| #define HAVE_STDLIB_H 1

| #define HAVE_STRING_H 1

| #define HAVE_MEMORY_H 1

| #define HAVE_STRINGS_H 1

| #define HAVE_INTTYPES_H 1

| #define HAVE_STDINT_H 1

| #define HAVE_UNISTD_H 1

| #define STDC_HEADERS 1

| #define HAVE_DLFCN_H 1

| #define LT_OBJDIR ".libs/"

| /* end confdefs.h.  */

| #include <ac_nonexistent.h>

configure:16217: checking for ld used by mpicxx

configure:16284: result: /usr/bin/ld -m elf_x86_64

configure:16291: checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld

configure:16306: result: yes

configure:16361: checking whether the mpicxx linker (/usr/bin/ld -m elf_x86_64) supports shared libraries

configure:17450: result: yes

configure:17486: mpicxx -c -g -O2 -I/gpfs_fs/home/rasegal/software/petsc/include conftest.cpp >&5

configure:17489: $? = 0

configure:17970: checking for mpicxx option to produce PIC

configure:17977: result: -fPIC -DPIC

configure:17985: checking if mpicxx PIC flag -fPIC -DPIC works

configure:18003: mpicxx -c -g -O2 -I/gpfs_fs/home/rasegal/software/petsc/include -fPIC -DPIC -DPIC conftest.cpp >&5

configure:18007: $? = 0

configure:18020: result: yes

configure:18043: checking if mpicxx static flag -static works

configure:18071: result: no

configure:18083: checking if mpicxx supports -c -o file.o

configure:18104: mpicxx -c -g -O2 -I/gpfs_fs/home/rasegal/software/petsc/include -o out/conftest2.o conftest.cpp >&5

configure:18108: $? = 0

configure:18130: result: yes

configure:18135: checking if mpicxx supports -c -o file.o

configure:18182: result: yes

configure:18212: checking whether the mpicxx linker (/usr/bin/ld -m elf_x86_64) supports shared libraries

configure:18252: result: yes

configure:18393: checking dynamic linker characteristics

configure:19146: result: GNU/Linux ld.so

configure:19211: checking how to hardcode library paths into programs

configure:19236: result: immediate

configure:19382: checking if libtool supports shared libraries

configure:19384: result: yes

configure:19387: checking whether to build shared libraries

configure:19411: result: yes

configure:19414: checking whether to build static libraries

configure:19418: result: yes

configure:19452: gfortran -c -g -O2  conftest.f >&5

configure:19455: $? = 0

configure:19915: checking for gfortran option to produce PIC

configure:19922: result: -fPIC

configure:19930: checking if gfortran PIC flag -fPIC works

configure:19948: gfortran -c -g -O2 -fPIC  conftest.f >&5

configure:19952: $? = 0

configure:19965: result: yes

configure:19988: checking if gfortran static flag -static works

configure:20016: result: no

configure:20028: checking if gfortran supports -c -o file.o

configure:20049: gfortran -c -g -O2 -o out/conftest2.o  conftest.f >&5

configure:20053: $? = 0

configure:20075: result: yes

configure:20080: checking if gfortran supports -c -o file.o

configure:20127: result: yes

configure:20157: checking whether the gfortran linker (/usr/bin/ld -m elf_x86_64) supports shared libraries

configure:21366: result: yes

configure:21507: checking dynamic linker characteristics

configure:22246: result: GNU/Linux ld.so

configure:22311: checking how to hardcode library paths into programs

configure:22336: result: immediate

configure:22386: checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld

configure:22401: result: yes

configure:22415: checking for gm4

configure:22445: result: no

configure:22415: checking for m4

configure:22431: found /usr/bin/m4

configure:22442: result: m4

configure:22456: checking for grep that handles long lines and -e

configure:22514: result: /bin/grep

configure:22519: checking for a sed that does not truncate output

configure:22583: result: /bin/sed

configure:22589: checking whether compiler supports __builtin_expect keyword

configure:22619: mpicxx -c -g -O2 -I/gpfs_fs/home/rasegal/software/petsc/include conftest.cpp >&5

configure:22619: $? = 0

configure:22622: result: yes

configure:22638: checking whether compiler supports __builtin_prefetch keyword

configure:22662: mpicxx -c -g -O2 -I/gpfs_fs/home/rasegal/software/petsc/include conftest.cpp >&5

configure:22662: $? = 0

configure:22665: result: yes

configure:22736: checking for ld used by mpicc

configure:22803: result: /usr/bin/ld -m elf_x86_64

configure:22810: checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld

configure:22825: result: yes

configure:22832: checking for shared library run path origin

configure:22845: result: done

configure:26550: Optional package libMesh is DISABLED

configure:26570: first check for a system Boost library; if not found, revert to bundled Boost library

configure: this is boost.m4 serial 26

configure:26590: Detected BOOST_ROOT; continuing with --with-boost=/gpfs_fs/home/rasegal/software/boost_1_66_0

configure:26600: checking for Boost headers version >= 1.57.0

configure:26679: mpicxx -c -g -O2 -I/gpfs_fs/home/rasegal/software/petsc/include -I/gpfs_fs/home/rasegal/software/boost_1_66

_0 conftest.cpp >&5

configure:26679: $? = 0

configure:26700: result: /gpfs_fs/home/rasegal/software/boost_1_66_0

configure:26723: checking for Boost's header version

configure:26754: result: 1_66

configure:26811: checking boost/array.hpp usability

configure:26811: mpicxx -c  -g -O2  -I/gpfs_fs/home/rasegal/software/petsc/include conftest.cpp >&5

configure:26811: $? = 0

configure:26811: result: yes

configure:26811: checking boost/array.hpp presence

configure:26811: mpicxx -E  -I/gpfs_fs/home/rasegal/software/petsc/include conftest.cpp

configure:26811: $? = 0

configure:26811: result: yes

configure:26811: checking for boost/array.hpp

configure:26811: result: yes

configure:26819: checking boost/multi_array.hpp usability

configure:26819: mpicxx -c  -g -O2  -I/gpfs_fs/home/rasegal/software/petsc/include conftest.cpp >&5

configure:26819: $? = 0

configure:26819: result: yes

configure:26819: checking boost/multi_array.hpp presence

configure:26819: mpicxx -E  -I/gpfs_fs/home/rasegal/software/petsc/include conftest.cpp

configure:26819: $? = 0

configure:26819: result: yes

configure:26819: checking for boost/multi_array.hpp

configure:26819: result: yes

configure:26874: first check for a system Eigen library; if not found, revert to bundled Eigen library

configure:26904: checking Eigen/Eigen usability

configure:26904: mpicxx -c   -g -O2  -I/gpfs_fs/home/rasegal/software/boost_1_66_0  -I/gpfs_fs/home/rasegal/software/boost_1

_66_0  -I/gpfs_fs/home/rasegal/software/petsc/include conftest.cpp >&5

conftest.cpp:64:23: error: Eigen/Eigen: No such file or directory

configure:26904: $? = 1

configure: failed program was:

| /* confdefs.h */

| #define PACKAGE_NAME "IBAMR"

| #define PACKAGE_TARNAME "IBAMR"

| #define PACKAGE_VERSION "171104"

| #define PACKAGE_STRING "IBAMR 171104"

| #define PACKAGE_BUGREPORT "boy...@gmail.com"

| #define PACKAGE_URL "https://ibamr.github.io"

| #define PACKAGE "IBAMR"

| #define VERSION "171104"

| #define FC_FUNC(name,NAME) name ## _

| #define FC_FUNC_(name,NAME) name ## _

| #define HAVE_MPI 1

| #define HAVE_MPI 1

| #define STDC_HEADERS 1

| #define HAVE_SYS_TYPES_H 1

| #define HAVE_SYS_STAT_H 1

| #define HAVE_STDLIB_H 1

| #define HAVE_STRING_H 1

| #define HAVE_MEMORY_H 1

| #define HAVE_STRINGS_H 1

| #define HAVE_INTTYPES_H 1

| #define HAVE_STDINT_H 1

| #define HAVE_UNISTD_H 1

| #define STDC_HEADERS 1

| #define HAVE_DLFCN_H 1

| #define LT_OBJDIR ".libs/"

| #define HAVE_BUILTIN_EXPECT 1

| #define HAVE_BUILTIN_PREFETCH 1

| #define HAVE_BOOST 1

| /* end confdefs.h.  */

| #include <stdio.h>

| #ifdef HAVE_SYS_TYPES_H

| # include <sys/types.h>

| #endif

| #ifdef HAVE_SYS_STAT_H

| # include <sys/stat.h>

| #endif

| #ifdef STDC_HEADERS

| # include <stdlib.h>

| # include <stddef.h>

| #else

| # ifdef HAVE_STDLIB_H

| #  include <stdlib.h>

| # endif

| #endif

| #ifdef HAVE_STRING_H

| # if !defined STDC_HEADERS && defined HAVE_MEMORY_H

| #  include <memory.h>

| # endif

| # include <string.h>

| #endif

| #ifdef HAVE_STRINGS_H

| # include <strings.h>

| #endif

| #ifdef HAVE_INTTYPES_H

| # include <inttypes.h>

| #endif

| #ifdef HAVE_STDINT_H

| # include <stdint.h>

| #endif

| #ifdef HAVE_UNISTD_H

| # include <unistd.h>

| #endif

| #include <Eigen/Eigen>

configure:26904: result: no

configure:26904: checking Eigen/Eigen presence

configure:26904: mpicxx -E  -I/gpfs_fs/home/rasegal/software/boost_1_66_0  -I/gpfs_fs/home/rasegal/software/boost_1_66_0  -I

/gpfs_fs/home/rasegal/software/petsc/include conftest.cpp

conftest.cpp:31:23: error: Eigen/Eigen: No such file or directory

configure:26904: $? = 1

configure: failed program was:

| /* confdefs.h */

| #define PACKAGE_NAME "IBAMR"

| #define PACKAGE_TARNAME "IBAMR"

| #define PACKAGE_VERSION "171104"

| #define PACKAGE_STRING "IBAMR 171104"

| #define PACKAGE_BUGREPORT "boy...@gmail.com"

| #define PACKAGE_URL "https://ibamr.github.io"

| #define PACKAGE "IBAMR"

| #define VERSION "171104"

| #define FC_FUNC(name,NAME) name ## _

| #define FC_FUNC_(name,NAME) name ## _

| #define HAVE_MPI 1

| #define HAVE_MPI 1

| #define STDC_HEADERS 1

| #define HAVE_SYS_TYPES_H 1

| #define HAVE_SYS_STAT_H 1

| #define HAVE_STDLIB_H 1

| #define HAVE_STRING_H 1

| #define HAVE_MEMORY_H 1

| #define HAVE_STRINGS_H 1

| #define HAVE_INTTYPES_H 1

| #define HAVE_STDINT_H 1

| #define HAVE_UNISTD_H 1

| #define STDC_HEADERS 1

| #define HAVE_DLFCN_H 1

| #define LT_OBJDIR ".libs/"

| #define HAVE_BUILTIN_EXPECT 1

| #define HAVE_BUILTIN_PREFETCH 1

| #define HAVE_BOOST 1

| /* end confdefs.h.  */

| #include <Eigen/Eigen>

configure:26904: result: no

configure:26904: checking for Eigen/Eigen

configure:26904: result: no

configure:26925: could not find system Eigen library, using bundled Eigen library

configure:26956: checking Eigen/Eigen usability

configure:26956: mpicxx -c   -g -O2 -I/gpfs_fs/home/rasegal/software/IBAMR/ibtk/contrib/eigen -I/gpfs_fs/home/rasegal/softwa

re/boost_1_66_0  -I/gpfs_fs/home/rasegal/software/boost_1_66_0  -I/gpfs_fs/home/rasegal/software/petsc/include conftest.cpp 

>&5

configure:26956: $? = 0

configure:26956: result: yes

configure:26956: checking Eigen/Eigen presence

configure:26956: mpicxx -E -I/gpfs_fs/home/rasegal/software/IBAMR/ibtk/contrib/eigen -I/gpfs_fs/home/rasegal/software/boost_

1_66_0  -I/gpfs_fs/home/rasegal/software/boost_1_66_0  -I/gpfs_fs/home/rasegal/software/petsc/include conftest.cpp

configure:26956: $? = 0

configure:26956: result: yes

configure:26956: checking for Eigen/Eigen

configure:26956: result: yes

configure:26995: checking for Eigen version >= 3.1.0

configure:27023: mpicxx -c  -g -O2 -I/gpfs_fs/home/rasegal/software/IBAMR/ibtk/contrib/eigen -I/gpfs_fs/home/rasegal/softwar

e/boost_1_66_0  -I/gpfs_fs/home/rasegal/software/petsc/include conftest.cpp >&5

configure:27023: $? = 0

configure:27029: result: yes

configure:27103: checking hdf5.h usability

configure:27103: mpicxx -c   -g -O2  -I/gpfs_fs/home/rasegal/software/IBAMR/ibtk/contrib/eigen -I/gpfs_fs/home/rasegal/softw

are/boost_1_66_0  -I/gpfs_fs/home/rasegal/software/boost_1_66_0  -I/gpfs_fs/home/rasegal/software/petsc/include conftest.cpp

 >&5

configure:27103: $? = 0

configure:27103: result: yes

configure:27103: checking hdf5.h presence

configure:27103: mpicxx -E  -I/gpfs_fs/home/rasegal/software/IBAMR/ibtk/contrib/eigen -I/gpfs_fs/home/rasegal/software/boost

_1_66_0  -I/gpfs_fs/home/rasegal/software/boost_1_66_0  -I/gpfs_fs/home/rasegal/software/petsc/include conftest.cpp

configure:27103: $? = 0

configure:27103: result: yes

configure:27103: checking for hdf5.h

configure:27103: result: yes

configure:27599: checking for libhdf5

configure:27629: mpicxx -o conftest   -g -O2  -I/gpfs_fs/home/rasegal/software/IBAMR/ibtk/contrib/eigen -I/gpfs_fs/home/rase

gal/software/boost_1_66_0  -I/gpfs_fs/home/rasegal/software/boost_1_66_0  -I/gpfs_fs/home/rasegal/software/petsc/include    

 conftest.cpp    -lhdf5 >&5

configure:27629: $? = 0

configure:27639: result: yes

configure:27646: checking how to link with libhdf5

configure:27648: result: -lhdf5

configure:28155: checking for libhdf5_hl

configure:28185: mpicxx -o conftest   -g -O2  -I/gpfs_fs/home/rasegal/software/IBAMR/ibtk/contrib/eigen -I/gpfs_fs/home/rase

gal/software/boost_1_66_0  -I/gpfs_fs/home/rasegal/software/boost_1_66_0  -I/gpfs_fs/home/rasegal/software/petsc/include    

 conftest.cpp -lhdf5    -lhdf5_hl >&5

configure:28185: $? = 0

configure:28195: result: yes

configure:28202: checking how to link with libhdf5_hl

configure:28204: result: -lhdf5_hl

configure:28233: checking for HDF5 version >= 1.8.7

configure:28261: mpicxx -c   -g -O2  -I/gpfs_fs/home/rasegal/software/IBAMR/ibtk/contrib/eigen -I/gpfs_fs/home/rasegal/softw

are/boost_1_66_0  -I/gpfs_fs/home/rasegal/software/boost_1_66_0  -I/gpfs_fs/home/rasegal/software/petsc/include conftest.cpp

 >&5

conftest.cpp:48:18: error: missing binary operator before token "("

conftest.cpp: In function 'int main()':

conftest.cpp:50: error: 'asdf' was not declared in this scope

configure:28261: $? = 1

configure: failed program was:

| /* confdefs.h */

| #define PACKAGE_NAME "IBAMR"

| #define PACKAGE_TARNAME "IBAMR"

| #define PACKAGE_VERSION "171104"

| #define PACKAGE_STRING "IBAMR 171104"

| #define PACKAGE_BUGREPORT "boy...@gmail.com"

| #define PACKAGE_URL "https://ibamr.github.io"

| #define PACKAGE "IBAMR"

| #define VERSION "171104"

| #define FC_FUNC(name,NAME) name ## _

| #define FC_FUNC_(name,NAME) name ## _

| #define HAVE_MPI 1

| #define HAVE_MPI 1

| #define STDC_HEADERS 1

| #define HAVE_SYS_TYPES_H 1

| #define HAVE_SYS_STAT_H 1

| #define HAVE_STDLIB_H 1

| #define HAVE_STRING_H 1

| #define HAVE_MEMORY_H 1

| #define HAVE_STRINGS_H 1

| #define HAVE_INTTYPES_H 1

| #define HAVE_STDINT_H 1

| #define HAVE_UNISTD_H 1

| #define STDC_HEADERS 1

| #define HAVE_DLFCN_H 1

| #define LT_OBJDIR ".libs/"

| #define HAVE_BUILTIN_EXPECT 1

| #define HAVE_BUILTIN_PREFETCH 1

| #define HAVE_BOOST 1

| #define HAVE_LIBHDF5 1

| #define HAVE_LIBHDF5_HL 1

| /* end confdefs.h.  */

| 

| #include <hdf5.h>

| 

| #ifdef FC_DUMMY_MAIN

| #ifndef FC_DUMMY_MAIN_EQ_F77

| #  ifdef __cplusplus

|      extern "C"

| #  endif

|    int FC_DUMMY_MAIN() { return 1; }

| #endif

| #endif

| int

| main ()

| {

| 

| #if H5_VERSION_GE(1,8,7)

| #else

| asdf

| #endif

| 

|   ;

|   return 0;

| }

configure:28267: result: no

configure:28270: WARNING: HDF5 versions prior to 1.8.7 are likely to be usable but are not officially supported

configure:28339: checking HYPRE.h usability

configure:28339: mpicxx -c   -g -O2 -I/gpfs_fs/home/rasegal/software/hypre/include  -I/gpfs_fs/home/rasegal/software/IBAMR/i

btk/contrib/eigen -I/gpfs_fs/home/rasegal/software/boost_1_66_0  -I/gpfs_fs/home/rasegal/software/boost_1_66_0  -I/gpfs_fs/h

ome/rasegal/software/petsc/include conftest.cpp >&5

configure:28339: $? = 0

configure:28339: result: yes

configure:28339: checking HYPRE.h presence

configure:28339: mpicxx -E -I/gpfs_fs/home/rasegal/software/hypre/include  -I/gpfs_fs/home/rasegal/software/IBAMR/ibtk/contr

ib/eigen -I/gpfs_fs/home/rasegal/software/boost_1_66_0  -I/gpfs_fs/home/rasegal/software/boost_1_66_0  -I/gpfs_fs/home/raseg

al/software/petsc/include conftest.cpp

configure:28339: $? = 0

configure:28339: result: yes

configure:28339: checking for HYPRE.h

configure:28339: result: yes

configure:28835: checking for libHYPRE

configure:28865: mpicxx -o conftest   -g -O2 -I/gpfs_fs/home/rasegal/software/hypre/include  -I/gpfs_fs/home/rasegal/softwar

e/IBAMR/ibtk/contrib/eigen -I/gpfs_fs/home/rasegal/software/boost_1_66_0  -I/gpfs_fs/home/rasegal/software/boost_1_66_0  -I/

gpfs_fs/home/rasegal/software/petsc/include -L/gpfs_fs/home/rasegal/software/hypre/lib     conftest.cpp /gpfs_fs/home/rasega

l/software/hypre/lib/libHYPRE.a -lhdf5_hl -lhdf5    >&5

configure:28865: $? = 0

configure:28875: result: yes

configure:28882: checking how to link with libHYPRE

configure:28884: result: /gpfs_fs/home/rasegal/software/hypre/lib/libHYPRE.a

configure:28967: first check for a system muParser library; if not found, revert to bundled muParser library

configure:28972: checking muParser.h usability

configure:28972: mpicxx -c   -g -O2  -I/gpfs_fs/home/rasegal/software/hypre/include  -I/gpfs_fs/home/rasegal/software/IBAMR/

ibtk/contrib/eigen -I/gpfs_fs/home/rasegal/software/boost_1_66_0  -I/gpfs_fs/home/rasegal/software/boost_1_66_0  -I/gpfs_fs/

home/rasegal/software/petsc/include conftest.cpp >&5

conftest.cpp:67:22: error: muParser.h: No such file or directory

configure:28972: $? = 1

configure: failed program was:

| /* confdefs.h */

| #define PACKAGE_NAME "IBAMR"

| #define PACKAGE_TARNAME "IBAMR"

| #define PACKAGE_VERSION "171104"

| #define PACKAGE_STRING "IBAMR 171104"

| #define PACKAGE_BUGREPORT "boy...@gmail.com"

| #define PACKAGE_URL "https://ibamr.github.io"

| #define PACKAGE "IBAMR"

| #define VERSION "171104"

| #define FC_FUNC(name,NAME) name ## _

| #define FC_FUNC_(name,NAME) name ## _

| #define HAVE_MPI 1

| #define HAVE_MPI 1

| #define STDC_HEADERS 1

| #define HAVE_SYS_TYPES_H 1

| #define HAVE_SYS_STAT_H 1

| #define HAVE_STDLIB_H 1

| #define HAVE_STRING_H 1

| #define HAVE_MEMORY_H 1

| #define HAVE_STRINGS_H 1

| #define HAVE_INTTYPES_H 1

| #define HAVE_STDINT_H 1

| #define HAVE_UNISTD_H 1

| #define STDC_HEADERS 1

| #define HAVE_DLFCN_H 1

| #define LT_OBJDIR ".libs/"

| #define HAVE_BUILTIN_EXPECT 1

| #define HAVE_BUILTIN_PREFETCH 1

| #define HAVE_BOOST 1

| #define HAVE_LIBHDF5 1

| #define HAVE_LIBHDF5_HL 1

| #define HAVE_LIBHYPRE 1

| /* end confdefs.h.  */

| #include <stdio.h>

| #ifdef HAVE_SYS_TYPES_H

| # include <sys/types.h>

| #endif

| #ifdef HAVE_SYS_STAT_H

| # include <sys/stat.h>

| #endif

| #ifdef STDC_HEADERS

| # include <stdlib.h>

| # include <stddef.h>

| #else

| # ifdef HAVE_STDLIB_H

| #  include <stdlib.h>

| # endif

| #endif

| #ifdef HAVE_STRING_H

| # if !defined STDC_HEADERS && defined HAVE_MEMORY_H

| #  include <memory.h>

| # endif

| # include <string.h>

| #endif

| #ifdef HAVE_STRINGS_H

| # include <strings.h>

| #endif

| #ifdef HAVE_INTTYPES_H

| # include <inttypes.h>

| #endif

| #ifdef HAVE_STDINT_H

| # include <stdint.h>

| #endif

| #ifdef HAVE_UNISTD_H

| # include <unistd.h>

| #endif

| #include <muParser.h>

configure:28972: result: no

configure:28972: checking muParser.h presence

configure:28972: mpicxx -E  -I/gpfs_fs/home/rasegal/software/hypre/include  -I/gpfs_fs/home/rasegal/software/IBAMR/ibtk/cont

rib/eigen -I/gpfs_fs/home/rasegal/software/boost_1_66_0  -I/gpfs_fs/home/rasegal/software/boost_1_66_0  -I/gpfs_fs/home/rase

gal/software/petsc/include conftest.cpp

conftest.cpp:34:22: error: muParser.h: No such file or directory

configure:28972: $? = 1

configure: failed program was:

| /* confdefs.h */

| #define PACKAGE_NAME "IBAMR"

| #define PACKAGE_TARNAME "IBAMR"

| #define PACKAGE_VERSION "171104"

| #define PACKAGE_STRING "IBAMR 171104"

| #define PACKAGE_BUGREPORT "boy...@gmail.com"

| #define PACKAGE_URL "https://ibamr.github.io"

| #define PACKAGE "IBAMR"

| #define VERSION "171104"

| #define FC_FUNC(name,NAME) name ## _

| #define FC_FUNC_(name,NAME) name ## _

| #define HAVE_MPI 1

| #define HAVE_MPI 1

| #define STDC_HEADERS 1

| #define HAVE_SYS_TYPES_H 1

| #define HAVE_SYS_STAT_H 1

| #define HAVE_STDLIB_H 1

| #define HAVE_STRING_H 1

| #define HAVE_MEMORY_H 1

| #define HAVE_STRINGS_H 1

| #define HAVE_INTTYPES_H 1

| #define HAVE_STDINT_H 1

| #define HAVE_UNISTD_H 1

| #define STDC_HEADERS 1

| #define HAVE_DLFCN_H 1

| #define LT_OBJDIR ".libs/"

| #define HAVE_BUILTIN_EXPECT 1

| #define HAVE_BUILTIN_PREFETCH 1

| #define HAVE_BOOST 1

| #define HAVE_LIBHDF5 1

| #define HAVE_LIBHDF5_HL 1

| #define HAVE_LIBHYPRE 1

| /* end confdefs.h.  */

| #include <muParser.h>

configure:28972: result: no

configure:28972: checking for muParser.h

configure:28972: result: no

configure:30115: could not find system muParser library, using bundled muParser library

configure:30124: checking muParser.h usability

configure:30124: mpicxx -c   -g -O2 -I/gpfs_fs/home/rasegal/software/IBAMR/ibtk/contrib/muparser/include -I/gpfs_fs/home/ras

egal/software/hypre/include  -I/gpfs_fs/home/rasegal/software/IBAMR/ibtk/contrib/eigen -I/gpfs_fs/home/rasegal/software/boos

t_1_66_0  -I/gpfs_fs/home/rasegal/software/boost_1_66_0  -I/gpfs_fs/home/rasegal/software/petsc/include conftest.cpp >&5

configure:30124: $? = 0

configure:30124: result: yes

configure:30124: checking muParser.h presence

configure:30124: mpicxx -E -I/gpfs_fs/home/rasegal/software/IBAMR/ibtk/contrib/muparser/include -I/gpfs_fs/home/rasegal/soft

ware/hypre/include  -I/gpfs_fs/home/rasegal/software/IBAMR/ibtk/contrib/eigen -I/gpfs_fs/home/rasegal/software/boost_1_66_0 

 -I/gpfs_fs/home/rasegal/software/boost_1_66_0  -I/gpfs_fs/home/rasegal/software/petsc/include conftest.cpp

configure:30124: $? = 0

configure:30124: result: yes

configure:30124: checking for muParser.h

configure:30124: result: yes

configure:30201: using PETSC_DIR: /gpfs_fs/home/rasegal/software/petsc

configure:30203: using PETSC_ARCH: arch-linux2-c-debug

configure:30212: checking petsc.h usability

configure:30212: mpicxx -c   -g -O2 -I/gpfs_fs/home/rasegal/software/petsc/include -I/gpfs_fs/home/rasegal/software/petsc/ar

ch-linux2-c-debug/include -I/gpfs_fs/home/rasegal/software/IBAMR/ibtk/contrib/muparser/include -I/gpfs_fs/home/rasegal/softw

are/hypre/include  -I/gpfs_fs/home/rasegal/software/IBAMR/ibtk/contrib/eigen -I/gpfs_fs/home/rasegal/software/boost_1_66_0  

-I/gpfs_fs/home/rasegal/software/boost_1_66_0  -I/gpfs_fs/home/rasegal/software/petsc/include conftest.cpp >&5

configure:30212: $? = 0

configure:30212: result: yes

configure:30212: checking petsc.h presence

configure:30212: mpicxx -E -I/gpfs_fs/home/rasegal/software/petsc/include -I/gpfs_fs/home/rasegal/software/petsc/arch-linux2

-c-debug/include -I/gpfs_fs/home/rasegal/software/IBAMR/ibtk/contrib/muparser/include -I/gpfs_fs/home/rasegal/software/hypre

/include  -I/gpfs_fs/home/rasegal/software/IBAMR/ibtk/contrib/eigen -I/gpfs_fs/home/rasegal/software/boost_1_66_0  -I/gpfs_f

s/home/rasegal/software/boost_1_66_0  -I/gpfs_fs/home/rasegal/software/petsc/include conftest.cpp

configure:30212: $? = 0

configure:30212: result: yes

configure:30212: checking for petsc.h

configure:30212: result: yes

configure:30221: checking for PETSc version 3.7 or 3.8

configure:30254: mpicxx -c   -g -O2 -I/gpfs_fs/home/rasegal/software/petsc/include -I/gpfs_fs/home/rasegal/software/petsc/ar

ch-linux2-c-debug/include -I/gpfs_fs/home/rasegal/software/IBAMR/ibtk/contrib/muparser/include -I/gpfs_fs/home/rasegal/softw

are/hypre/include  -I/gpfs_fs/home/rasegal/software/IBAMR/ibtk/contrib/eigen -I/gpfs_fs/home/rasegal/software/boost_1_66_0  

-I/gpfs_fs/home/rasegal/software/boost_1_66_0  -I/gpfs_fs/home/rasegal/software/petsc/include conftest.cpp >&5

configure:30254: $? = 0

configure:30260: result: yes

configure:30753: checking for libpetsc

configure:30783: mpicxx -o conftest   -g -O2 -I/gpfs_fs/home/rasegal/software/petsc/include -I/gpfs_fs/home/rasegal/software

/petsc/arch-linux2-c-debug/include -I/gpfs_fs/home/rasegal/software/IBAMR/ibtk/contrib/muparser/include -I/gpfs_fs/home/rase

gal/software/hypre/include  -I/gpfs_fs/home/rasegal/software/IBAMR/ibtk/contrib/eigen -I/gpfs_fs/home/rasegal/software/boost

_1_66_0  -I/gpfs_fs/home/rasegal/software/boost_1_66_0  -I/gpfs_fs/home/rasegal/software/petsc/include  -L/gpfs_fs/home/rase

gal/software/hypre/lib     conftest.cpp -Wl,-rpath,/usr/mpi/gcc/openmpi-1.10.4/lib64 -L/usr/mpi/gcc/openmpi-1.10.4/lib64 -Wl

,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.4.7 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7 -llapack -lblas -lX11 -lmpi_usempi -

lmpi_mpifh -lgfortran -lm -lmpi_cxx -lstdc++ -lm -lmpi_cxx -lstdc++ -lm -ldl -lmpi -lgcc_s -lpthread -ldl /gpfs_fs/home/rase

gal/software/hypre/lib/libHYPRE.a -lhdf5_hl -lhdf5    -lpetsc >&5

/usr/bin/ld: cannot find -lpetsc

collect2: ld returned 1 exit status

configure:30783: $? = 1

configure: failed program was:

| /* confdefs.h */

| #define PACKAGE_NAME "IBAMR"

| #define PACKAGE_TARNAME "IBAMR"

| #define PACKAGE_VERSION "171104"

| #define PACKAGE_STRING "IBAMR 171104"

| #define PACKAGE_BUGREPORT "boy...@gmail.com"

| #define PACKAGE_URL "https://ibamr.github.io"

| #define PACKAGE "IBAMR"

| #define VERSION "171104"

| #define FC_FUNC(name,NAME) name ## _

| #define FC_FUNC_(name,NAME) name ## _

| #define HAVE_MPI 1

| #define HAVE_MPI 1

| #define STDC_HEADERS 1

| #define HAVE_SYS_TYPES_H 1

| #define HAVE_SYS_STAT_H 1

| #define HAVE_STDLIB_H 1

| #define HAVE_STRING_H 1

| #define HAVE_MEMORY_H 1

| #define HAVE_STRINGS_H 1

| #define HAVE_INTTYPES_H 1

| #define HAVE_STDINT_H 1

| #define HAVE_UNISTD_H 1

| #define STDC_HEADERS 1

| #define HAVE_DLFCN_H 1

| #define LT_OBJDIR ".libs/"

| #define HAVE_BUILTIN_EXPECT 1

| #define HAVE_BUILTIN_PREFETCH 1

| #define HAVE_BOOST 1

| #define HAVE_LIBHDF5 1

| #define HAVE_LIBHDF5_HL 1

| #define HAVE_LIBHYPRE 1

| #define HAVE_LIBMUPARSER 1

| /* end confdefs.h.  */

| 

| #ifdef FC_DUMMY_MAIN

| #ifndef FC_DUMMY_MAIN_EQ_F77

| #  ifdef __cplusplus

|      extern "C"

| #  endif

|    int FC_DUMMY_MAIN() { return 1; }

| #endif

| #endif

| int

| main ()

| {

| 

|   ;

|   return 0;

| }

configure:30793: result: no

configure:30819: error: could not find working libpetsc


## ---------------- ##

## Cache variables. ##

## ---------------- ##


ac_cv_build=x86_64-pc-linux-gnu

ac_cv_c_compiler_gnu=yes

ac_cv_cxx_compiler_gnu=yes

ac_cv_env_BOOST_ROOT_set=set

ac_cv_env_BOOST_ROOT_value=/gpfs_fs/home/rasegal/software/boost_1_66_0

ac_cv_env_CCC_set=

ac_cv_env_CCC_value=

ac_cv_env_CC_set=set

ac_cv_env_CC_value=mpicc

ac_cv_env_CFLAGS_set=

ac_cv_env_CFLAGS_value=

ac_cv_env_CPPFLAGS_set=set

ac_cv_env_CPPFLAGS_value=-I/gpfs_fs/home/rasegal/software/petsc/include

ac_cv_env_CPP_set=

ac_cv_env_CPP_value=

ac_cv_env_CXXCPP_set=

ac_cv_env_CXXCPP_value=

ac_cv_env_CXXFLAGS_set=

ac_cv_env_CXXFLAGS_value=

ac_cv_env_CXX_set=set

ac_cv_env_CXX_value=mpicxx

ac_cv_env_FCFLAGS_set=

ac_cv_env_FCFLAGS_value=

ac_cv_env_FCLIBS_set=

ac_cv_env_FCLIBS_value=

ac_cv_env_FC_set=

ac_cv_env_FC_value=

ac_cv_env_LDFLAGS_set=

ac_cv_env_LDFLAGS_value=

ac_cv_env_LIBS_set=

ac_cv_env_LIBS_value=

ac_cv_env_LT_SYS_LIBRARY_PATH_set=

ac_cv_env_LT_SYS_LIBRARY_PATH_value=

ac_cv_env_MPICC_set=

ac_cv_env_MPICC_value=

ac_cv_env_MPICXX_set=

ac_cv_env_MPICXX_value=

ac_cv_env_PETSC_ARCH_set=set

ac_cv_env_PETSC_ARCH_value=arch-linux2-c-debug

ac_cv_env_PETSC_DIR_set=set

ac_cv_env_PETSC_DIR_value=/gpfs_fs/home/rasegal/software/petsc

ac_cv_env_build_alias_set=

ac_cv_env_build_alias_value=

ac_cv_env_host_alias_set=

ac_cv_env_host_alias_value=

ac_cv_env_target_alias_set=

ac_cv_env_target_alias_value=

ac_cv_fc_compiler_gnu=yes

ac_cv_fc_dummy_main=none

ac_cv_fc_libs=' -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64 -L/lib/.

./lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../.. -lgfortranbegin -lgfortran -lm'

ac_cv_fc_mangling='lower case, underscore, no extra underscore'

ac_cv_fc_srcext_f=none

ac_cv_fortran_dummy_main=none

ac_cv_header_Eigen_Eigen=yes

ac_cv_header_HYPRE_h=yes

ac_cv_header_boost_array_hpp=yes

ac_cv_header_boost_multi_array_hpp=yes

ac_cv_header_dlfcn_h=yes

ac_cv_header_hdf5_h=yes

ac_cv_header_inttypes_h=yes

ac_cv_header_memory_h=yes

ac_cv_header_muParser_h=yes

ac_cv_header_petsc_h=yes

ac_cv_header_stdc=yes

ac_cv_header_stdint_h=yes

ac_cv_header_stdlib_h=yes

ac_cv_header_string_h=yes

ac_cv_header_strings_h=yes

ac_cv_header_sys_stat_h=yes

ac_cv_header_sys_types_h=yes

ac_cv_header_sys_types_h_makedev=yes

ac_cv_header_unistd_h=yes

ac_cv_host=x86_64-pc-linux-gnu

ac_cv_libHYPRE=yes

ac_cv_libhdf5=yes

ac_cv_libhdf5_hl=yes

ac_cv_libpetsc=no

ac_cv_objext=o

ac_cv_path_EGREP='/bin/grep -E'

ac_cv_path_FGREP='/bin/grep -F'

ac_cv_path_GREP=/bin/grep

ac_cv_path_SED=/bin/sed

ac_cv_path_install='/usr/bin/install -c'

ac_cv_path_lt_DD=/bin/dd

ac_cv_path_mkdir=/bin/mkdir

ac_cv_prog_AWK=gawk

ac_cv_prog_CPP='mpicc -E'

ac_cv_prog_CXXCPP='mpicxx -E'

ac_cv_prog_M4=m4

ac_cv_prog_ac_ct_AR=ar

ac_cv_prog_ac_ct_CC=mpicc

ac_cv_prog_ac_ct_FC=gfortran

ac_cv_prog_ac_ct_OBJDUMP=objdump

ac_cv_prog_ac_ct_RANLIB=ranlib

ac_cv_prog_ac_ct_STRIP=strip

ac_cv_prog_cc_c89=

ac_cv_prog_cc_g=yes

ac_cv_prog_cxx_g=yes

ac_cv_prog_fc_g=yes

ac_cv_prog_fc_v=-v

ac_cv_prog_make_make_set=yes

acl_cv_hardcode_direct=no

acl_cv_hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir'

acl_cv_hardcode_libdir_separator=

acl_cv_hardcode_minus_L=no

acl_cv_libext=a

acl_cv_libname_spec='lib$name'

acl_cv_library_names_spec='$libname$shrext'

acl_cv_path_LD='/usr/bin/ld -m elf_x86_64'

acl_cv_prog_gnu_ld=yes

acl_cv_rpath=done

acl_cv_shlibext=so

acl_cv_wl=-Wl,

am_cv_CC_dependencies_compiler_type=gcc3

am_cv_CXX_dependencies_compiler_type=gcc3

am_cv_make_support_nested_variables=yes

am_cv_prog_cc_c_o=yes

boost_cv_inc_path=/gpfs_fs/home/rasegal/software/boost_1_66_0

boost_cv_lib_version=1_66

lt_cv_ar_at_file=@

lt_cv_archive_cmds_need_lc=no

lt_cv_deplibs_check_method=pass_all

lt_cv_file_magic_cmd='$MAGIC_CMD'

lt_cv_file_magic_test_file=

lt_cv_ld_reload_flag=-r

lt_cv_nm_interface='BSD nm'

lt_cv_objdir=.libs

lt_cv_path_LD=/usr/bin/ld

lt_cv_path_LDCXX='/usr/bin/ld -m elf_x86_64'

lt_cv_path_NM='/usr/bin/nm -B'

lt_cv_path_mainfest_tool=no

lt_cv_prog_compiler_c_o=yes

lt_cv_prog_compiler_c_o_CXX=yes

lt_cv_prog_compiler_c_o_FC=yes

lt_cv_prog_compiler_pic='-fPIC -DPIC'

lt_cv_prog_compiler_pic_CXX='-fPIC -DPIC'

lt_cv_prog_compiler_pic_FC=-fPIC

lt_cv_prog_compiler_pic_works=yes

lt_cv_prog_compiler_pic_works_CXX=yes

lt_cv_prog_compiler_pic_works_FC=yes

lt_cv_prog_compiler_rtti_exceptions=no

lt_cv_prog_compiler_static_works=no

lt_cv_prog_compiler_static_works_CXX=no

lt_cv_prog_compiler_static_works_FC=no

lt_cv_prog_gnu_ld=yes

lt_cv_prog_gnu_ldcxx=yes

lt_cv_sharedlib_from_linklib_cmd='printf %s\n'

lt_cv_shlibpath_overrides_runpath=yes

lt_cv_sys_global_symbol_pipe='sed -n -e '\''s/^.*[ ]\([ABCDGIRSTW][ABCDGIRSTW]*\)[ ][ ]*\([_A-Za-z][_A-Za

-z0-9]*\)$/\1 \2 \2/p'\'' | sed '\''/ __gnu_lto/d'\'''

lt_cv_sys_global_symbol_to_c_name_address='sed -n -e '\''s/^: \(.*\) .*$/  {"\1", (void *) 0},/p'\'' -e '\''s/^[ABCDGIRSTW][

ABCDGIRSTW]* .* \(.*\)$/  {"\1", (void *) \&\1},/p'\'''

lt_cv_sys_global_symbol_to_c_name_address_lib_prefix='sed -n -e '\''s/^: \(.*\) .*$/  {"\1", (void *) 0},/p'\'' -e '\''s/^[A

BCDGIRSTW][ABCDGIRSTW]* .* \(lib.*\)$/  {"\1", (void *) \&\1},/p'\'' -e '\''s/^[ABCDGIRSTW][ABCDGIRSTW]* .* \(.*\)$/  {"lib\

1", (void *) \&\1},/p'\'''

lt_cv_sys_global_symbol_to_cdecl='sed -n -e '\''s/^T .* \(.*\)$/extern int \1();/p'\'' -e '\''s/^[ABCDGIRSTW][ABCDGIRSTW]* .

* \(.*\)$/extern char \1;/p'\'''

lt_cv_sys_global_symbol_to_import=

lt_cv_sys_max_cmd_len=1966080

lt_cv_to_host_file_cmd=func_convert_file_noop

lt_cv_to_tool_file_cmd=func_convert_file_noop

lt_cv_truncate_bin='/bin/dd bs=4096 count=1'


## ----------------- ##

## Output variables. ##

## ----------------- ##


ACLOCAL='${SHELL} /gpfs_fs/home/rasegal/software/IBAMR/config/missing aclocal-1.15'

AMDEPBACKSLASH='\'

AMDEP_FALSE='#'

AMDEP_TRUE=''

AMTAR='$${TAR-tar}'

AM_BACKSLASH='\'

AM_DEFAULT_V='$(AM_DEFAULT_VERBOSITY)'

AM_DEFAULT_VERBOSITY='0'

AM_V='$(V)'

AR='ar'

AUTOCONF='${SHELL} /gpfs_fs/home/rasegal/software/IBAMR/config/missing autoconf'

AUTOHEADER='${SHELL} /gpfs_fs/home/rasegal/software/IBAMR/config/missing autoheader'

AUTOMAKE='${SHELL} /gpfs_fs/home/rasegal/software/IBAMR/config/missing automake-1.15'

AWK='gawk'

BOOST_CPPFLAGS='-I/gpfs_fs/home/rasegal/software/boost_1_66_0'

BOOST_ROOT='/gpfs_fs/home/rasegal/software/boost_1_66_0'

CC='mpicc'

CCDEPMODE='depmode=gcc3'

CFLAGS='  -g -O2'

CPP='mpicc -E'

CPPFLAGS='-I/gpfs_fs/home/rasegal/software/petsc/include -I/gpfs_fs/home/rasegal/software/petsc/arch-linux2-c-debug/include 

-I/gpfs_fs/home/rasegal/software/IBAMR/ibtk/contrib/muparser/include -I/gpfs_fs/home/rasegal/software/hypre/include  -I/gpfs

_fs/home/rasegal/software/IBAMR/ibtk/contrib/eigen -I/gpfs_fs/home/rasegal/software/boost_1_66_0  -I/gpfs_fs/home/rasegal/so

ftware/boost_1_66_0  -I/gpfs_fs/home/rasegal/software/petsc/include'

CXX='mpicxx'

CXXCPP='mpicxx -E'

CXXDEPMODE='depmode=gcc3'

CXXFLAGS='  -g -O2'

CYGPATH_W='echo'

DEFS=''

DEPDIR='.deps'

DISTCHECK_CONFIGURE_FLAGS=' '\''--with-boost=/gpfs_fs/home/rasegal/software/boost_1_66_0'\'''

DLLTOOL='false'

DSYMUTIL=''

DUMPBIN=''

ECHO_C=''

ECHO_N='-n'

ECHO_T=''

EGREP='/bin/grep -E'

EXEEXT=''

F77='gfortran'

FC='gfortran'

FCFLAGS='  -g -O2'

FCFLAGS_f=''

FCLIBS='   -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64 -L/lib/../lib

64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../.. -lgfortranbegin -lgfortran -lm'

FFLAGS='-g -O2'

FGREP='/bin/grep -F'

FLIBS=' -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64 -L/lib/../lib64 

-L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../.. -lgfortranbegin -lgfortran -lm'

GREP='/bin/grep'

GSL_ENABLED_FALSE=''

GSL_ENABLED_TRUE=''

GTEST_ENABLED_FALSE=''

GTEST_ENABLED_TRUE=''

HAVE_LIBGSL=''

HAVE_LIBGSLCBLAS=''

HAVE_LIBGTEST=''

HAVE_LIBHDF5='yes'

HAVE_LIBHDF5_HL='yes'

HAVE_LIBHYPRE='yes'

HAVE_LIBMESH_DBG=''

HAVE_LIBMESH_DEVEL=''

HAVE_LIBMESH_OPROF=''

HAVE_LIBMESH_OPT=''

HAVE_LIBMESH_PROF=''

HAVE_LIBMUPARSER=''

HAVE_LIBNETCDF=''

HAVE_LIBPETSC='no'

HAVE_LIBSAMRAI2D_ALGS=''

HAVE_LIBSAMRAI2D_APPU=''

HAVE_LIBSAMRAI2D_GEOM=''

HAVE_LIBSAMRAI2D_HIER=''

HAVE_LIBSAMRAI2D_MATH_STD=''

HAVE_LIBSAMRAI2D_MESH=''

HAVE_LIBSAMRAI2D_PDAT_STD=''

HAVE_LIBSAMRAI2D_SOLV=''

HAVE_LIBSAMRAI2D_XFER=''

HAVE_LIBSAMRAI3D_ALGS=''

HAVE_LIBSAMRAI3D_APPU=''

HAVE_LIBSAMRAI3D_GEOM=''

HAVE_LIBSAMRAI3D_HIER=''

HAVE_LIBSAMRAI3D_MATH_STD=''

HAVE_LIBSAMRAI3D_MESH=''

HAVE_LIBSAMRAI3D_PDAT_STD=''

HAVE_LIBSAMRAI3D_SOLV=''

HAVE_LIBSAMRAI3D_XFER=''

HAVE_LIBSAMRAI=''

HAVE_LIBSILO=''

HAVE_LIBSILOH5=''

INSTALL_DATA='${INSTALL} -m 644'

INSTALL_PROGRAM='${INSTALL}'

INSTALL_SCRIPT='${INSTALL}'

INSTALL_STRIP_PROGRAM='$(install_sh) -c -s'

LD='/usr/bin/ld -m elf_x86_64'

LDFLAGS=' -L/gpfs_fs/home/rasegal/software/hypre/lib    '

LIBGSL=''

LIBGSLCBLAS=''

LIBGSLCBLAS_PREFIX=''

LIBGSL_PREFIX=''

LIBGTEST=''

LIBGTEST_PREFIX=''

LIBHDF5='-lhdf5'

LIBHDF5_HL='-lhdf5_hl'

LIBHDF5_HL_PREFIX=''

LIBHDF5_PREFIX=''

LIBHYPRE='/gpfs_fs/home/rasegal/software/hypre/lib/libHYPRE.a'

LIBHYPRE_PREFIX=''

LIBMESH_CONFIG=''

LIBMESH_DBG=''

LIBMESH_DBG_PREFIX=''

LIBMESH_DEVEL=''

LIBMESH_DEVEL_PREFIX=''

LIBMESH_ENABLED_FALSE=''

LIBMESH_ENABLED_TRUE='#'

LIBMESH_OPROF=''

LIBMESH_OPROF_PREFIX=''

LIBMESH_OPT=''

LIBMESH_OPT_PREFIX=''

LIBMESH_PROF=''

LIBMESH_PROF_PREFIX=''

LIBMUPARSER='$(abs_top_builddir)/ibtk/contrib/muparser/lib/libmuparser.a'

LIBMUPARSER_PREFIX=''

LIBNETCDF=''

LIBNETCDF_PREFIX=''

LIBOBJS=''

LIBPETSC=''

LIBPETSC_PREFIX=''

LIBS='-Wl,-rpath,/usr/mpi/gcc/openmpi-1.10.4/lib64 -L/usr/mpi/gcc/openmpi-1.10.4/lib64 -Wl,-rpath,/usr/lib/gcc/x86_64-redhat

-linux/4.4.7 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7 -llapack -lblas -lX11 -lmpi_usempi -lmpi_mpifh -lgfortran -lm -lmpi_cx

x -lstdc++ -lm -lmpi_cxx -lstdc++ -lm -ldl -lmpi -lgcc_s -lpthread -ldl /gpfs_fs/home/rasegal/software/hypre/lib/libHYPRE.a 

-lhdf5_hl -lhdf5   '

LIBSAMRAI2D_ALGS=''

LIBSAMRAI2D_ALGS_PREFIX=''

LIBSAMRAI2D_APPU=''

LIBSAMRAI2D_APPU_PREFIX=''

LIBSAMRAI2D_GEOM=''

LIBSAMRAI2D_GEOM_PREFIX=''

LIBSAMRAI2D_HIER=''

LIBSAMRAI2D_HIER_PREFIX=''

LIBSAMRAI2D_MATH_STD=''

LIBSAMRAI2D_MATH_STD_PREFIX=''

LIBSAMRAI2D_MESH=''

LIBSAMRAI2D_MESH_PREFIX=''

LIBSAMRAI2D_PDAT_STD=''

LIBSAMRAI2D_PDAT_STD_PREFIX=''

LIBSAMRAI2D_SOLV=''

LIBSAMRAI2D_SOLV_PREFIX=''

LIBSAMRAI2D_XFER=''

LIBSAMRAI2D_XFER_PREFIX=''

LIBSAMRAI3D_ALGS=''

LIBSAMRAI3D_ALGS_PREFIX=''

LIBSAMRAI3D_APPU=''

LIBSAMRAI3D_APPU_PREFIX=''

LIBSAMRAI3D_GEOM=''

LIBSAMRAI3D_GEOM_PREFIX=''

LIBSAMRAI3D_HIER=''

LIBSAMRAI3D_HIER_PREFIX=''

LIBSAMRAI3D_MATH_STD=''

LIBSAMRAI3D_MATH_STD_PREFIX=''

LIBSAMRAI3D_MESH=''

LIBSAMRAI3D_MESH_PREFIX=''

LIBSAMRAI3D_PDAT_STD=''

LIBSAMRAI3D_PDAT_STD_PREFIX=''

LIBSAMRAI3D_SOLV=''

LIBSAMRAI3D_SOLV_PREFIX=''

LIBSAMRAI3D_XFER=''

LIBSAMRAI3D_XFER_PREFIX=''

LIBSAMRAI=''

LIBSAMRAI_PREFIX=''

LIBSILO=''

LIBSILOH5=''

LIBSILOH5_PREFIX=''

LIBSILO_PREFIX=''

LIBTOOL='$(SHELL) $(top_builddir)/libtool'

LIPO=''

LN_S='ln -s'

LTLIBGSL=''

LTLIBGSLCBLAS=''

LTLIBGTEST=''

LTLIBHDF5='-lhdf5'

LTLIBHDF5_HL='-lhdf5_hl'

LTLIBHYPRE='-L/gpfs_fs/home/rasegal/software/hypre/lib -lHYPRE'

LTLIBMESH_DBG=''

LTLIBMESH_DEVEL=''

LTLIBMESH_OPROF=''

LTLIBMESH_OPT=''

LTLIBMESH_PROF=''

LTLIBMUPARSER=''

LTLIBNETCDF=''

LTLIBOBJS=''

LTLIBPETSC=''

LTLIBSAMRAI2D_ALGS=''

LTLIBSAMRAI2D_APPU=''

LTLIBSAMRAI2D_GEOM=''

LTLIBSAMRAI2D_HIER=''

LTLIBSAMRAI2D_MATH_STD=''

LTLIBSAMRAI2D_MESH=''

LTLIBSAMRAI2D_PDAT_STD=''

LTLIBSAMRAI2D_SOLV=''

LTLIBSAMRAI2D_XFER=''

LTLIBSAMRAI3D_ALGS=''

LTLIBSAMRAI3D_APPU=''

LTLIBSAMRAI3D_GEOM=''

LTLIBSAMRAI3D_HIER=''

LTLIBSAMRAI3D_MATH_STD=''

LTLIBSAMRAI3D_MESH=''

LTLIBSAMRAI3D_PDAT_STD=''

LTLIBSAMRAI3D_SOLV=''

LTLIBSAMRAI3D_XFER=''

LTLIBSAMRAI=''

LTLIBSILO=''

LTLIBSILOH5=''

LT_SYS_LIBRARY_PATH=''

M4='m4'

MAINT='#'

MAINTAINER_MODE_FALSE=''

MAINTAINER_MODE_TRUE='#'

MAKEINFO='${SHELL} /gpfs_fs/home/rasegal/software/IBAMR/config/missing makeinfo'

MANIFEST_TOOL=':'

MKDIR_P='/bin/mkdir -p'

MPICC=''

MPICXX=''

NM='/usr/bin/nm -B'

NMEDIT=''

OBJDUMP='objdump'

OBJEXT='o'

OTOOL64=''

OTOOL=''

PACKAGE='IBAMR'

PACKAGE_BUGREPORT='boy...@gmail.com'

PACKAGE_CFLAGS=''

PACKAGE_CONTRIB_LIBS='$(abs_top_builddir)/ibtk/contrib/muparser/lib/libmuparser.a '

PACKAGE_CPPFLAGS='-I/gpfs_fs/home/rasegal/software/IBAMR/ibtk/contrib/muparser/include -I/gpfs_fs/home/rasegal/software/hypr

e/include  -I/gpfs_fs/home/rasegal/software/IBAMR/ibtk/contrib/eigen -I/gpfs_fs/home/rasegal/software/boost_1_66_0 '

PACKAGE_CXXFLAGS=''

PACKAGE_FCFLAGS=''

PACKAGE_LDFLAGS=' -L/gpfs_fs/home/rasegal/software/hypre/lib  '

PACKAGE_LIBS='/gpfs_fs/home/rasegal/software/hypre/lib/libHYPRE.a -lhdf5_hl -lhdf5 '

PACKAGE_NAME='IBAMR'

PACKAGE_STRING='IBAMR 171104'

PACKAGE_TARNAME='IBAMR'

PACKAGE_URL='https://ibamr.github.io'

PACKAGE_VERSION='171104'

PATH_SEPARATOR=':'

PETSC_ARCH='arch-linux2-c-debug'

PETSC_DIR='/gpfs_fs/home/rasegal/software/petsc'

RANLIB='ranlib'

SAMRAI2D_ENABLED_FALSE=''

SAMRAI2D_ENABLED_TRUE=''

SAMRAI3D_ENABLED_FALSE=''

SAMRAI3D_ENABLED_TRUE=''

SAMRAI_DIR=''

SAMRAI_FORTDIR=''

SED='/bin/sed'

SET_MAKE=''

SHELL='/bin/sh'

SILO_ENABLED_FALSE=''

SILO_ENABLED_TRUE=''

STRIP='strip'

USING_BUNDLED_EIGEN_FALSE='#'

USING_BUNDLED_EIGEN_TRUE=''

USING_BUNDLED_MUPARSER_FALSE='#'

USING_BUNDLED_MUPARSER_TRUE=''

VERSION='171104'

ac_ct_AR='ar'

ac_ct_CC='mpicc'

ac_ct_CXX=''

ac_ct_DUMPBIN=''

ac_ct_FC='gfortran'

am__EXEEXT_FALSE=''

am__EXEEXT_TRUE=''

am__fastdepCC_FALSE='#'

am__fastdepCC_TRUE=''

am__fastdepCXX_FALSE='#'

am__fastdepCXX_TRUE=''

am__include='include'

am__isrc=''

am__leading_dot='.'

am__nodep='_no'

am__quote=''

am__tar='$${TAR-tar} chof - "$$tardir"'

am__untar='$${TAR-tar} xf -'

bindir='${exec_prefix}/bin'

build='x86_64-pc-linux-gnu'

build_alias=''

build_cpu='x86_64'

build_os='linux-gnu'

build_vendor='pc'

datadir='${datarootdir}'

datarootdir='${prefix}/share'

docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'

dvidir='${docdir}'

exec_prefix='NONE'

host='x86_64-pc-linux-gnu'

host_alias=''

host_cpu='x86_64'

host_os='linux-gnu'

host_vendor='pc'

htmldir='${docdir}'

includedir='${prefix}/include'

infodir='${datarootdir}/info'

install_sh='${SHELL} /gpfs_fs/home/rasegal/software/IBAMR/config/install-sh'

libdir='${exec_prefix}/lib'

libexecdir='${exec_prefix}/libexec'

localedir='${datarootdir}/locale'

localstatedir='${prefix}/var'

mandir='${datarootdir}/man'

mkdir_p='$(MKDIR_P)'

oldincludedir='/usr/include'

pdfdir='${docdir}'

prefix='NONE'

program_transform_name='s,x,x,'

psdir='${docdir}'

sbindir='${exec_prefix}/sbin'

sharedstatedir='${prefix}/com'

subdirs=''

sysconfdir='${prefix}/etc'

target_alias=''


## ----------- ##

## confdefs.h. ##

## ----------- ##


/* confdefs.h */

#define PACKAGE_NAME "IBAMR"

#define PACKAGE_TARNAME "IBAMR"

#define PACKAGE_VERSION "171104"

#define PACKAGE_STRING "IBAMR 171104"

#define PACKAGE_BUGREPORT "boy...@gmail.com"

#define PACKAGE_URL "https://ibamr.github.io"

#define PACKAGE "IBAMR"

#define VERSION "171104"

#define FC_FUNC(name,NAME) name ## _

#define FC_FUNC_(name,NAME) name ## _

#define HAVE_MPI 1

#define HAVE_MPI 1

#define STDC_HEADERS 1

#define HAVE_SYS_TYPES_H 1

#define HAVE_SYS_STAT_H 1

#define HAVE_STDLIB_H 1

#define HAVE_STRING_H 1

#define HAVE_MEMORY_H 1

#define HAVE_STRINGS_H 1

#define HAVE_INTTYPES_H 1

#define HAVE_STDINT_H 1

#define HAVE_UNISTD_H 1

#define STDC_HEADERS 1

#define HAVE_DLFCN_H 1

#define LT_OBJDIR ".libs/"

#define HAVE_BUILTIN_EXPECT 1

#define HAVE_BUILTIN_PREFETCH 1

#define HAVE_BOOST 1

#define HAVE_LIBHDF5 1

#define HAVE_LIBHDF5_HL 1

#define HAVE_LIBHYPRE 1

#define HAVE_LIBMUPARSER 1


configure: exit 1

jmda...@vcu.edu

unread,
Mar 9, 2018, 5:12:33 PM3/9/18
to IBAMR Users
The configuration is erroring at libpetsc.

Shashank Acharya

unread,
Mar 9, 2018, 7:37:47 PM3/9/18
to IBAMR Users
Looks like Eigen is missing and PETSc options are incomplete.

I'm attaching my IBAMR install script. You can review the options in it or just straight-up execute it. Keep hitting enter while periodically checking the output for errors.

You need to provide your own system MPI.

If this doesn't work, someone else who's more familiar will help you out.

| ...
install_dbg_opt_IBAMR-master_on_NUIT_Quest.sh

Boyce Griffith

unread,
Mar 9, 2018, 8:58:42 PM3/9/18
to ibamr...@googlegroups.com
It looks like the linker is not able to find PETSc in the specified location.

Can you send the output of:

ls /gpfs_fs/home/rasegal/software/petsc/arch-linux2-c-debug/lib
> --
> You received this message because you are subscribed to the Google Groups "IBAMR Users" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to ibamr-users...@googlegroups.com.
> To post to this group, send email to ibamr...@googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.

jmda...@vcu.edu

unread,
Mar 12, 2018, 10:24:23 AM3/12/18
to IBAMR Users
Boyce, 

Here is the output you requested. 

ls /gpfs_fs/home/rasegal/software/petsc/arch-linux2-c-debug/lib 

libpetsc.so  libpetsc.so.3.8  libpetsc.so.3.8.3  petsc pkgconfig

| ...

jmda...@vcu.edu

unread,
Mar 13, 2018, 2:55:38 PM3/13/18
to IBAMR Users
The install script worked. The issue that I was experiencing was not realizing the intrdependencies of the dependencies. 

Thanks to all for the help. 





Boyce Griffith

unread,
Mar 14, 2018, 8:57:11 AM3/14/18
to ibamr...@googlegroups.com

On Mar 13, 2018, at 1:54 PM, jmda...@vcu.edu wrote:

The install script worked. The issue that I was experiencing was not realizing the intrdependencies of the dependencies. 

What steps did you do "out of order"?

And, does everything now seem to be working?

Thanks to all for the help. 






jmda...@vcu.edu

unread,
Mar 14, 2018, 1:57:29 PM3/14/18
to IBAMR Users


When I used the Install script the install ran. It used a different order than what I had used, it used a 3.75 version of Petsc, and it explicitly installed everything rather than allowing IBAMR to install it's included versions. I noted that when it was running there were interdependencies between some of the libraries. 

I was installing on Centos 6. 

Shashank Acharya

unread,
Mar 14, 2018, 2:15:46 PM3/14/18
to IBAMR Users
Thanks for testing the script... Its a simple script and I usually work with Ubuntu but I'm glad to see that it worked out of the box on another linux flavor without any hiccups.
Reply all
Reply to author
Forward
0 new messages