Re: [plumed-users] Installing PLUMED 2.2.2 HREX on NERSC's Cori (KNL): can't find MPI

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Giovanni Bussi

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Oct 3, 2017, 12:34:46 PM10/3/17
to plumed...@googlegroups.com
Hi,

I cannot see why your configure script is failing. It might be not related to plumed. Notice that:
1. PLUMED 2.2 is not supported. Please switch to PLUMED 2.3 which, by the way, incorporates the hrex changes in the GROMACS 5.1.4 patch (in case you need those)
2. Which is the problem with cross compiling? If you mean that you can't use "plumed patch", please notice that "plumed-patch" works also when cross compiling.
3. From the log you attached it looks like <mpi.h> was found and MPI was enabled

Giovanni
 

On Tue, Oct 3, 2017 at 6:25 PM, Sean Marks <seanma...@gmail.com> wrote:
Hello, PLUMED community,

I'm trying to install Giovanni Bussi's HREX fork of PLUMED 2.2.2 on NERSC's new platform, Cori, on the Knight's Landing (KNL) nodes. I'm running into some issues configuring with MPI support: When PLUMED attempts to compile and run some test scripts, the #include <mpi.h> directive appears to be failing.

My Approach:
To hopefully avoid some issues which can come up when cross-compiling, I am attempting to install PLUMED on a KNL node directly via a Slurm job. As instructed in a seminar I attended on using Cori, I switch over to the Cray KNL module (craype-mic-knl,below) which is supposed automagically provide the correct MPI compilers.

I suspect that this is an issue with PLUMED's configure script (hence my message on this forum), but if that's not the case, I will gladly take my concerns to the NERSC help desk instead.

Input/Output
Here is my configure script that I submit to a KNL node, attempting to configure PLUMED:

#!/bin/bash -l

#SBATCH --partition=debug
#SBATCH --nodes=1
#SBATCH -t 00:05:00
#SBATCH -L SCRATCH
#SBATCH -C knl

numProcessors=8

##########################
### Set up directories ###
##########################

# Where to install PLUMED
export plumed_install_dir="$HOME/programs/knl/plumed/2.2.2/hrex/mpi/shared"

# Home directory of PLUMED tar ball/zip archive
plumed_dir=plumed2-2.2-hrex

#################
### Compilers ###
#################

# Compile for KNL, not Haswell
module swap craype-haswell craype-mic-knl
export CC=cc
export CXX=CC
export MPICC=cc
export MPICXX=CC

##########################
### External libraries ###
##########################

# None at the moment

############################
### Configure with cmake ###
############################

cd $plumed_dir

make clean

# Configure from main directory
./configure --prefix=${plumed_install_dir} \
            --enable-modules=crystallization \
            --program-suffix=_mpi \
            --disable-basic-warnings

Here is the resulting config.log:

This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.

It was created by PLUMED configure 2, which was
generated by GNU Autoconf 2.69.  Invocation command line was

  $ ./configure --prefix=/global/homes/s/smarks/programs/knl/plumed/2.2.2/hrex/mpi/shared --enable-modules=crystallization --program-suffix=_mpi --disable-basic-warnings

## --------- ##
## Platform. ##
## --------- ##

hostname = nid04598
uname -m = x86_64
uname -r = 4.4.49-92.11.1_3.0-cray_ari_c
uname -s = Linux
uname -v = #1 SMP Mon Aug 14 21:49:55 UTC 2017 (3.0.89)

/usr/bin/uname -p = x86_64
/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/common/software/bin
PATH: /usr/common/mss/bin
PATH: /usr/common/nsg/bin
PATH: /opt/cray/pe/fftw/3.3.4.6/mic_knl/bin
PATH: /opt/cray/pe/fftw/3.3.4.6/haswell/bin
PATH: /usr/common/software/darshan/3.1.4/bin
PATH: /usr/common/software/altd/2.0/bin
PATH: /usr/common/software/bin
PATH: /usr/common/mss/bin
PATH: /usr/common/nsg/bin
PATH: /opt/cray/pe/mpt/7.6.0/gni/bin
PATH: /opt/cray/rca/2.2.11-6.0.4.0_13.2__g84de67a.ari/bin
PATH: /opt/cray/alps/6.4.1-6.0.4.0_7.2__g86d0f3d.ari/sbin
PATH: /opt/cray/job/2.2.2-6.0.4.0_8.2__g3c644b5.ari/bin
PATH: /opt/cray/pe/craype/2.5.12/bin
PATH: /opt/intel/compilers_and_libraries_2017.2.174/linux/bin/intel64
PATH: /usr/syscom/nsg/sbin
PATH: /usr/syscom/nsg/bin
PATH: /opt/cray/pe/modules/3.2.10.6/bin
PATH: /usr/local/bin
PATH: /usr/bin
PATH: /bin
PATH: /usr/bin/X11
PATH: /usr/games
PATH: /usr/lib/mit/bin
PATH: /usr/lib/mit/sbin
PATH: /opt/cray/pe/bin


## ----------- ##
## Core tests. ##
## ----------- ##

configure:2391: Enabling module crystallization
configure:3010: checking for C++ compiler version
configure:3019: CC --version >&5
icpc (ICC) 17.0.2 20170213
Copyright (C) 1985-2017 Intel Corporation.  All rights reserved.

configure:3030: $? = 0
configure:3019: CC -v >&5
icpc: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance
icpc: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance
icpc: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance
icpc: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance
icpc version 17.0.2 (gcc version 4.8.0 compatibility)
ld    /usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../lib64/crt1.o /usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../lib64/crti.o /usr/lib64/gcc/x86_64-suse-linux/4.8/crtbeginT.o --build-id -static -m elf_x86_64 -L/opt/cray/pe/fftw/3.3.4.6/mic_knl/lib -L/opt/cray/pe/mpt/7.6.0/gni/sma/lib64 -L/opt/cray/pe/libsci/17.06.1/INTEL/16.0/x86_64/lib -L/opt/cray/dmapp/default/lib64 -L/opt/cray/pe/mpt/7.6.0/gni/mpich-intel/16.0/lib -L/opt/cray/dmapp/default/lib64 -L/opt/cray/pe/mpt/7.6.0/gni/mpich-intel/16.0/lib -L/usr/common/software/darshan/3.1.4/lib -L/opt/cray/rca/2.2.11-6.0.4.0_13.2__g84de67a.ari/lib64 -L/opt/cray/alps/6.4.1-6.0.4.0_7.2__g86d0f3d.ari/lib64 -L/opt/cray/xpmem/2.2.2-6.0.4.0_3.1__g43b0535.ari/lib64 -L/opt/cray/dmapp/7.1.1-6.0.4.0_46.2__gb8abda2.ari/lib64 -L/opt/cray/pe/pmi/5.0.12/lib64 -L/opt/cray/ugni/6.0.14-6.0.4.0_14.1__ge7db4a2.ari/lib64 -L/opt/cray/udreg/2.3.2-6.0.4.0_12.2__g2f9c3ee.ari/lib64 -L/opt/cray/pe/atp/2.1.1/libApp -L/lib64 -L/opt/cray/wlm_detect/1.2.1-6.0.4.0_22.1__gd26a3dc.ari/lib64 -o a.out -L/opt/intel/compilers_and_libraries_2017.2.174/linux/compiler/lib/intel64 -L/opt/intel/compilers_and_libraries_2017.2.174/linux/mkl/lib/intel64 -L/opt/intel/compilers_and_libraries_2017.2.174/linux/compiler/lib/intel64_lin -L/usr/lib64/gcc/x86_64-suse-linux/4.8/ -L/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../lib64 -L/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../lib64/ -L/lib/../lib64 -L/lib/../lib64/ -L/usr/lib/../lib64 -L/usr/lib/../lib64/ -L/opt/intel/compilers_and_libraries_2017.2.174/linux/compiler/lib/intel64/ -L/opt/intel/compilers_and_libraries_2017.2.174/linux/mkl/lib/intel64/ -L/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/lib/ -L/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../ -L/lib64 -L/lib/ -L/usr/lib64 -L/usr/lib -lfftw3f_mpi -lfftw3f_threads -lfftw3f -lfftw3_mpi -lfftw3_threads -lfftw3 @/usr/common/software/darshan/3.1.4/share/ld-opts/darshan-base-ld-opts -lfmpich -lmpichcxx --start-group -ldarshan -ldarshan-stubs --end-group -lz --no-as-needed -lAtpSigHandler -lAtpSigHCommData --undefined=_ATP_Data_Globals --undefined=__atpHandlerInstall -lpthread -lmpichcxx_intel -lrt -lugni -lpthread -lpmi -L/opt/intel/compilers_and_libraries_2017.2.174/linux/compiler/lib/intel64_lin -limf -lm -ldl -lsma -lpmi -ldmapp -lpthread -lsci_intel_mpi -lsci_intel -L/opt/intel/compilers_and_libraries_2017.2.174/linux/compiler/lib/intel64_lin -limf -lm -ldl -lmpich_intel -lrt -lugni -lpthread -lpmi -L/opt/intel/compilers_and_libraries_2017.2.174/linux/compiler/lib/intel64_lin -limf -lm -ldl -lpmi -lpthread -lalpslli -lpthread -lwlm_detect -lalpsutil -lpthread -lrca -lxpmem -lugni -lpthread -ludreg -lsci_intel -L/opt/intel/compilers_and_libraries_2017.2.174/linux/compiler/lib/intel64_lin -limf -lm -lpthread -ldl -lhugetlbfs --as-needed -lstdc++ --no-as-needed --as-needed -limf --no-as-needed --as-needed -lm --no-as-needed --as-needed -lifcore --no-as-needed --as-needed -lifport --no-as-needed --as-needed -lpthread --no-as-needed -limf -lsvml -lirng -lstdc++ -lm -lipgo -ldecimal -lstdc++ -lgcc -lgcc_eh -lirc -lsvml -lc -lgcc -lgcc_eh -lirc_s -ldl -lc /usr/lib64/gcc/x86_64-suse-linux/4.8/crtend.o /usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../lib64/crtn.o
/opt/intel/compilers_and_libraries_2017.2.174/linux/compiler/lib/intel64/libifcore.a(for_main.o): In function `main':
for_main.c:(.text+0x3e): undefined reference to `MAIN__'
/usr/bin/ld: link errors found, deleting executable `a.out'
configure:3030: $? = 1
configure:3019: CC -V >&5
Intel(R) C++ Intel(R) 64 Compiler for applications running on Intel(R) 64, Version 17.0.2.174 Build 20170213
Copyright (C) 1985-2017 Intel Corporation.  All rights reserved.

configure:3030: $? = 0
configure:3019: CC -qversion >&5
icpc: command line warning #10006: ignoring unknown option '-qversion'
icpc: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance
icpc: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance
icpc: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance
icpc: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance
/opt/intel/compilers_and_libraries_2017.2.174/linux/compiler/lib/intel64/libifcore.a(for_main.o): In function `main':
for_main.c:(.text+0x3e): undefined reference to `MAIN__'
/usr/bin/ld: link errors found, deleting executable `a.out'
configure:3030: $? = 1
configure:3050: checking whether the C++ compiler works
configure:3072: CC -O   conftest.cpp  >&5
configure:3076: $? = 0
configure:3124: result: yes
configure:3127: checking for C++ compiler default output file name
configure:3129: result: a.out
configure:3135: checking for suffix of executables
configure:3142: CC -o conftest -O   conftest.cpp  >&5
configure:3146: $? = 0
configure:3168: result:
configure:3190: checking whether we are cross compiling
configure:3198: CC -o conftest -O   conftest.cpp  >&5
configure:3202: $? = 0
configure:3209: ./conftest
Tue Oct  3 08:59:26 2017: [unset]:_pmi_alps_get_apid:alps response not OKAY
Tue Oct  3 08:59:26 2017: [unset]:_pmi_init:_pmi_alps_init returned -1
configure:3213: $? = 0
configure:3228: result: no
configure:3233: checking for suffix of object files
configure:3255: CC -c -O  conftest.cpp >&5
configure:3259: $? = 0
configure:3280: result: o
configure:3284: checking whether we are using the GNU C++ compiler
configure:3303: CC -c -O  conftest.cpp >&5
configure:3303: $? = 0
configure:3312: result: yes
configure:3321: checking whether CC accepts -g
configure:3341: CC -c -g  conftest.cpp >&5
configure:3341: $? = 0
configure:3382: result: yes
configure:3455: checking for gcc
configure:3482: result: cc
configure:3711: checking for C compiler version
configure:3720: cc --version >&5
icc (ICC) 17.0.2 20170213
Copyright (C) 1985-2017 Intel Corporation.  All rights reserved.

configure:3731: $? = 0
configure:3720: cc -v >&5
icc: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance
icc: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance
icc: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance
icc version 17.0.2 (gcc version 4.8.0 compatibility)
ld    /usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../lib64/crt1.o /usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../lib64/crti.o /usr/lib64/gcc/x86_64-suse-linux/4.8/crtbeginT.o --build-id -static -m elf_x86_64 -L/opt/cray/pe/fftw/3.3.4.6/mic_knl/lib -L/opt/cray/pe/mpt/7.6.0/gni/sma/lib64 -L/opt/cray/pe/libsci/17.06.1/INTEL/16.0/x86_64/lib -L/opt/cray/dmapp/default/lib64 -L/opt/cray/pe/mpt/7.6.0/gni/mpich-intel/16.0/lib -L/usr/common/software/darshan/3.1.4/lib -L/opt/cray/rca/2.2.11-6.0.4.0_13.2__g84de67a.ari/lib64 -L/opt/cray/alps/6.4.1-6.0.4.0_7.2__g86d0f3d.ari/lib64 -L/opt/cray/xpmem/2.2.2-6.0.4.0_3.1__g43b0535.ari/lib64 -L/opt/cray/dmapp/7.1.1-6.0.4.0_46.2__gb8abda2.ari/lib64 -L/opt/cray/pe/pmi/5.0.12/lib64 -L/opt/cray/ugni/6.0.14-6.0.4.0_14.1__ge7db4a2.ari/lib64 -L/opt/cray/udreg/2.3.2-6.0.4.0_12.2__g2f9c3ee.ari/lib64 -L/opt/cray/pe/atp/2.1.1/libApp -L/lib64 -L/opt/cray/wlm_detect/1.2.1-6.0.4.0_22.1__gd26a3dc.ari/lib64 -o a.out -L/opt/intel/compilers_and_libraries_2017.2.174/linux/compiler/lib/intel64 -L/opt/intel/compilers_and_libraries_2017.2.174/linux/mkl/lib/intel64 -L/opt/intel/compilers_and_libraries_2017.2.174/linux/compiler/lib/intel64_lin -L/usr/lib64/gcc/x86_64-suse-linux/4.8/ -L/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../lib64 -L/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../lib64/ -L/lib/../lib64 -L/lib/../lib64/ -L/usr/lib/../lib64 -L/usr/lib/../lib64/ -L/opt/intel/compilers_and_libraries_2017.2.174/linux/compiler/lib/intel64/ -L/opt/intel/compilers_and_libraries_2017.2.174/linux/mkl/lib/intel64/ -L/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/lib/ -L/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../ -L/lib64 -L/lib/ -L/usr/lib64 -L/usr/lib -lfftw3f_mpi -lfftw3f_threads -lfftw3f -lfftw3_mpi -lfftw3_threads -lfftw3 @/usr/common/software/darshan/3.1.4/share/ld-opts/darshan-base-ld-opts -lfmpich -lmpichcxx --start-group -ldarshan -ldarshan-stubs --end-group -lz --no-as-needed -lAtpSigHandler -lAtpSigHCommData --undefined=_ATP_Data_Globals --undefined=__atpHandlerInstall -lpthread -lsma -lpmi -ldmapp -lpthread -lsci_intel_mpi -lsci_intel -L/opt/intel/compilers_and_libraries_2017.2.174/linux/compiler/lib/intel64_lin -limf -lm -ldl -lmpich_intel -lrt -lugni -lpthread -lpmi -L/opt/intel/compilers_and_libraries_2017.2.174/linux/compiler/lib/intel64_lin -limf -lm -ldl -lpmi -lpthread -lalpslli -lpthread -lwlm_detect -lalpsutil -lpthread -lrca -lxpmem -lugni -lpthread -ludreg -lsci_intel -L/opt/intel/compilers_and_libraries_2017.2.174/linux/compiler/lib/intel64_lin -limf -lm -lpthread -ldl -lhugetlbfs --as-needed -limf --no-as-needed --as-needed -lm --no-as-needed --as-needed -lifcore --no-as-needed --as-needed -lifport --no-as-needed --as-needed -lpthread --no-as-needed -limf -lsvml -lirng -lm -lipgo -ldecimal -lgcc -lgcc_eh -lirc -lsvml -lc -lgcc -lgcc_eh -lirc_s -ldl -lc /usr/lib64/gcc/x86_64-suse-linux/4.8/crtend.o /usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../lib64/crtn.o
/opt/intel/compilers_and_libraries_2017.2.174/linux/compiler/lib/intel64/libifcore.a(for_main.o): In function `main':
for_main.c:(.text+0x3e): undefined reference to `MAIN__'
/usr/bin/ld: link errors found, deleting executable `a.out'
configure:3731: $? = 1
configure:3720: cc -V >&5
Intel(R) C Intel(R) 64 Compiler for applications running on Intel(R) 64, Version 17.0.2.174 Build 20170213
Copyright (C) 1985-2017 Intel Corporation.  All rights reserved.

configure:3731: $? = 0
configure:3720: cc -qversion >&5
icc: command line warning #10006: ignoring unknown option '-qversion'
icc: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance
icc: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance
icc: warning #10315: specifying -lm before files may supersede the Intel(R) math library and affect performance
/opt/intel/compilers_and_libraries_2017.2.174/linux/compiler/lib/intel64/libifcore.a(for_main.o): In function `main':
for_main.c:(.text+0x3e): undefined reference to `MAIN__'
/usr/bin/ld: link errors found, deleting executable `a.out'
configure:3731: $? = 1
configure:3735: checking whether we are using the GNU C compiler
configure:3754: cc -c   conftest.c >&5
configure:3754: $? = 0
configure:3763: result: yes
configure:3772: checking whether cc accepts -g
configure:3792: cc -c -g  conftest.c >&5
configure:3792: $? = 0
configure:3833: result: yes
configure:3850: checking for cc option to accept ISO C89
configure:3913: cc  -c -g -O2  conftest.c >&5
configure:3913: $? = 0
configure:3926: result: none needed
configure:4004: checking for gfortran
configure:4034: result: no
configure:4004: checking for g95
configure:4034: result: no
configure:4004: checking for xlf95
configure:4034: result: no
configure:4004: checking for f95
configure:4034: result: no
configure:4004: checking for fort
configure:4034: result: no
configure:4004: checking for ifort
configure:4020: found /opt/intel/compilers_and_libraries_2017.2.174/linux/bin/intel64/ifort
configure:4031: result: ifort
configure:4057: checking for Fortran compiler version
configure:4066: ifort --version >&5
ifort (IFORT) 17.0.2 20170213
Copyright (C) 1985-2017 Intel Corporation.  All rights reserved.

configure:4077: $? = 0
configure:4066: ifort -v >&5
ifort version 17.0.2
configure:4077: $? = 0
configure:4066: ifort -V >&5
Intel(R) Fortran Intel(R) 64 Compiler for applications running on Intel(R) 64, Version 17.0.2.174 Build 20170213
Copyright (C) 1985-2017 Intel Corporation.  All rights reserved.

configure:4077: $? = 0
configure:4066: ifort -qversion >&5
ifort: command line warning #10006: ignoring unknown option '-qversion'
ifort: command line error: no files specified; for help type "ifort -help"
configure:4077: $? = 1
configure:4086: checking whether we are using the GNU Fortran compiler
configure:4099: ifort -c   conftest.F >&5
conftest.F(3): error #5082: Syntax error, found END-OF-STATEMENT when expecting one of: => = . [ % ( :
       choke me
---------------^
compilation aborted for conftest.F (code 1)
configure:4099: $? = 1
configure: failed program was:
|       program main
| #ifndef __GNUC__
|        choke me
| #endif
|
|       end
configure:4108: result: no
configure:4114: checking whether ifort accepts -g
configure:4125: ifort -c -g  conftest.f >&5
configure:4125: $? = 0
configure:4133: result: yes
configure:4174: Initial CXX:         CC
configure:4176: Initial CXXFLAGS:    -O
configure:4178: Initial CPPFLAGS:   
configure:4180: Initial CFLAGS:      -g -O2
configure:4182: Initial LDFLAGS:    
configure:4184: Initial LIBS:       
configure:4186: Initial STATIC_LIBS:
configure:4188: Initial LD:          CC
configure:4190: Initial LDSO:        CC
configure:4192: Initial SOEXT:      
configure:4202: checking whether CC accepts -fPIC
configure:4215: CC -c -O -fPIC  conftest.cpp >&5
configure:4215: $? = 0
configure:4228: CC -o conftest -O -fPIC   conftest.cpp  >&5
configure:4228: $? = 0
configure:4229: result: yes
configure:4255: checking whether cc accepts -fPIC
configure:4268: cc -c -g -O2 -fPIC  conftest.c >&5
configure:4268: $? = 0
configure:4281: cc -o conftest -g -O2 -fPIC   conftest.c  >&5
configure:4281: $? = 0
configure:4282: result: yes
configure:4962: checking whether CC supports explicit
configure:4975: CC -c -O -fPIC  conftest.cpp >&5
configure:4975: $? = 0
configure:4976: result: yes
configure:4989: Now we will check compulsory headers and libraries
configure:4996: checking how to run the C++ preprocessor
configure:5023: CC -E  conftest.cpp
configure:5023: $? = 0
configure:5037: CC -E  conftest.cpp
conftest.cpp(9): error #2379: cannot open source file "ac_nonexistent.h"
  #include <ac_nonexistent.h>
                             ^

configure:5037: $? = 2
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "PLUMED"
| #define PACKAGE_TARNAME "plumed"
| #define PACKAGE_VERSION "2"
| #define PACKAGE_STRING "PLUMED 2"
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE_URL ""
| /* end confdefs.h.  */
| #include <ac_nonexistent.h>
configure:5062: result: CC -E
configure:5082: CC -E  conftest.cpp
configure:5082: $? = 0
configure:5096: CC -E  conftest.cpp
conftest.cpp(9): error #2379: cannot open source file "ac_nonexistent.h"
  #include <ac_nonexistent.h>
                             ^

configure:5096: $? = 2
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "PLUMED"
| #define PACKAGE_TARNAME "plumed"
| #define PACKAGE_VERSION "2"
| #define PACKAGE_STRING "PLUMED 2"
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE_URL ""
| /* end confdefs.h.  */
| #include <ac_nonexistent.h>
configure:5125: checking for grep that handles long lines and -e
configure:5183: result: /usr/bin/grep
configure:5188: checking for egrep
configure:5250: result: /usr/bin/grep -E
configure:5255: checking for ANSI C header files
configure:5275: CC -c -O -fPIC  conftest.cpp >&5
configure:5275: $? = 0
configure:5348: CC -o conftest -O -fPIC   conftest.cpp  >&5
configure:5348: $? = 0
configure:5348: ./conftest
Tue Oct  3 09:01:16 2017: [unset]:_pmi_alps_get_apid:alps response not OKAY
Tue Oct  3 09:01:16 2017: [unset]:_pmi_init:_pmi_alps_init returned -1
configure:5348: $? = 0
configure:5359: result: yes
configure:5372: checking for sys/types.h
configure:5372: CC -c -O -fPIC  conftest.cpp >&5
configure:5372: $? = 0
configure:5372: result: yes
configure:5372: checking for sys/stat.h
configure:5372: CC -c -O -fPIC  conftest.cpp >&5
configure:5372: $? = 0
configure:5372: result: yes
configure:5372: checking for stdlib.h
configure:5372: CC -c -O -fPIC  conftest.cpp >&5
configure:5372: $? = 0
configure:5372: result: yes
configure:5372: checking for string.h
configure:5372: CC -c -O -fPIC  conftest.cpp >&5
configure:5372: $? = 0
configure:5372: result: yes
configure:5372: checking for memory.h
configure:5372: CC -c -O -fPIC  conftest.cpp >&5
configure:5372: $? = 0
configure:5372: result: yes
configure:5372: checking for strings.h
configure:5372: CC -c -O -fPIC  conftest.cpp >&5
configure:5372: $? = 0
configure:5372: result: yes
configure:5372: checking for inttypes.h
configure:5372: CC -c -O -fPIC  conftest.cpp >&5
configure:5372: $? = 0
configure:5372: result: yes
configure:5372: checking for stdint.h
configure:5372: CC -c -O -fPIC  conftest.cpp >&5
configure:5372: $? = 0
configure:5372: result: yes
configure:5372: checking for unistd.h
configure:5372: CC -c -O -fPIC  conftest.cpp >&5
configure:5372: $? = 0
configure:5372: result: yes
configure:5384: checking dirent.h usability
configure:5384: CC -c -O -fPIC  conftest.cpp >&5
configure:5384: $? = 0
configure:5384: result: yes
configure:5384: checking dirent.h presence
configure:5384: CC -E  conftest.cpp
configure:5384: $? = 0
configure:5384: result: yes
configure:5384: checking for dirent.h
configure:5384: result: yes
configure:5392: checking for readdir
configure:5392: CC -o conftest -O -fPIC   conftest.cpp  >&5
configure:5392: $? = 0
configure:5392: result: yes
configure:5419: checking for dgemv
configure:5419: CC -o conftest -O -fPIC   conftest.cpp  >&5
/tmp/icpcFfNwwq.o: In function `main':
conftest.cpp:(.text+0x35): undefined reference to `dgemv'
/usr/bin/ld: link errors found, deleting executable `conftest'
configure:5419: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "PLUMED"
| #define PACKAGE_TARNAME "plumed"
| #define PACKAGE_VERSION "2"
| #define PACKAGE_STRING "PLUMED 2"
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE_URL ""
| #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
| /* end confdefs.h.  */
| /* Define dgemv to an innocuous variant, in case <limits.h> declares dgemv.
|    For example, HP-UX 11i <limits.h> declares gettimeofday.  */
| #define dgemv innocuous_dgemv
|
| /* System header to define __stub macros and hopefully few prototypes,
|     which can conflict with char dgemv (); below.
|     Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
|     <limits.h> exists even on freestanding compilers.  */
|
| #ifdef __STDC__
| # include <limits.h>
| #else
| # include <assert.h>
| #endif
|
| #undef dgemv
|
| /* 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 dgemv ();
| /* The GNU C library defines this for functions which it implements
|     to always fail with ENOSYS.  Some functions are actually named
|     something starting with __ and the normal name is an alias.  */
| #if defined __stub_dgemv || defined __stub___dgemv
| choke me
| #endif
|
| int
| main ()
| {
| return dgemv ();
|   ;
|   return 0;
| }
configure:5419: result: no
configure:5424: checking for dgemv_
configure:5424: CC -o conftest -O -fPIC   conftest.cpp  >&5
configure:5424: $? = 0
configure:5424: result: yes
configure:5541: checking for dsyevr_
configure:5541: CC -o conftest -O -fPIC   conftest.cpp  >&5
configure:5541: $? = 0
configure:5541: result: yes
configure:5619: Now we will check for optional headers and libraries
configure:5641: checking for molfile_dcdplugin_init in -lmolfile_plugin
configure:5666: CC -o conftest -O -fPIC   conftest.cpp -lmolfile_plugin   >&5
/usr/bin/ld: cannot find -lmolfile_plugin
configure:5666: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "PLUMED"
| #define PACKAGE_TARNAME "plumed"
| #define PACKAGE_VERSION "2"
| #define PACKAGE_STRING "PLUMED 2"
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE_URL ""
| #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 __PLUMED_HAS_EXTERNAL_BLAS 1
| #define __PLUMED_HAS_EXTERNAL_LAPACK 1
| #define __PLUMED_HAS_MOLFILE_PLUGINS 1
| /* 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 molfile_dcdplugin_init ();
| int
| main ()
| {
| return molfile_dcdplugin_init ();
|   ;
|   return 0;
| }
configure:5675: result: no
configure:5688: WARNING: using internal molfile_plugins, which only support dcd/xtc/trr/trj/crd files
configure:5702: checking for dlopen in -ldl
configure:5727: CC -o conftest -O -fPIC   conftest.cpp -ldl   >&5
/tmp/icpc8RBIEd.o: In function `main':
conftest.cpp:(.text+0x35): warning: Using 'dlopen' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking
configure:5727: $? = 0
configure:5736: result: yes
configure:5748: checking mpi.h usability
configure:5748: CC -c -O -fPIC  conftest.cpp >&5
configure:5748: $? = 0
configure:5748: result: yes
configure:5748: checking mpi.h presence
configure:5748: CC -E  conftest.cpp
configure:5748: $? = 0
configure:5748: result: yes
configure:5748: checking for mpi.h
configure:5748: result: yes
configure:5751: checking for MPI_Init
configure:5751: CC -o conftest -O -fPIC   conftest.cpp -ldl  >&5
configure:5751: $? = 0
configure:5751: result: yes
configure:5785: checking for CC option to support OpenMP
configure:5800: CC -o conftest -O -fPIC   conftest.cpp -ldl  >&5

## ---------------- ##
## Cache variables. ##
## ---------------- ##

ac_cv_c_compiler_gnu=yes
ac_cv_cxx_compiler_gnu=yes
ac_cv_env_CCC_set=
ac_cv_env_CCC_value=
ac_cv_env_CC_set=set
ac_cv_env_CC_value=cc
ac_cv_env_CFLAGS_set=
ac_cv_env_CFLAGS_value=
ac_cv_env_CPPFLAGS_set=
ac_cv_env_CPPFLAGS_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=CC
ac_cv_env_FCFLAGS_set=
ac_cv_env_FCFLAGS_value=
ac_cv_env_FC_set=
ac_cv_env_FC_value=
ac_cv_env_LDFLAGS_set=
ac_cv_env_LDFLAGS_value=
ac_cv_env_LDSO_set=
ac_cv_env_LDSO_value=
ac_cv_env_LIBS_set=
ac_cv_env_LIBS_value=
ac_cv_env_SOEXT_set=
ac_cv_env_SOEXT_value=
ac_cv_env_STATIC_LIBS_set=
ac_cv_env_STATIC_LIBS_value=
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=no
ac_cv_func_MPI_Init=yes
ac_cv_func_dgemv=no
ac_cv_func_dgemv_=yes
ac_cv_func_dsyevr_=yes
ac_cv_func_readdir=yes
ac_cv_header_dirent_h=yes
ac_cv_header_inttypes_h=yes
ac_cv_header_memory_h=yes
ac_cv_header_mpi_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_unistd_h=yes
ac_cv_lib_dl_dlopen=yes
ac_cv_lib_molfile_plugin_molfile_dcdplugin_init=no
ac_cv_objext=o
ac_cv_path_EGREP='/usr/bin/grep -E'
ac_cv_path_GREP=/usr/bin/grep
ac_cv_prog_CXXCPP='CC -E'
ac_cv_prog_ac_ct_CC=cc
ac_cv_prog_ac_ct_FC=ifort
ac_cv_prog_cc_c89=
ac_cv_prog_cc_g=yes
ac_cv_prog_cxx_g=yes
ac_cv_prog_fc_g=yes

## ----------------- ##
## Output variables. ##
## ----------------- ##

CC='cc'
CFLAGS='-g -O2 -fPIC'
CPPFLAGS=''
CXX='CC'
CXXCPP='CC -E'
CXXFLAGS='-O -fPIC'
DEFS=''
ECHO_C=''
ECHO_N='-n'
ECHO_T=''
EGREP='/usr/bin/grep -E'
EXEEXT=''
FC='ifort'
FCFLAGS='-g'
GREP='/usr/bin/grep'
LD='CC'
LDFLAGS=''
LDSO='CC'
LD_RO=''
LIBOBJS=''
LIBS='-ldl '
LTLIBOBJS=''
OBJEXT='o'
OPENMP_CXXFLAGS=''
PACKAGE_BUGREPORT=''
PACKAGE_NAME='PLUMED'
PACKAGE_STRING='PLUMED 2'
PACKAGE_TARNAME='plumed'
PACKAGE_URL=''
PACKAGE_VERSION='2'
PATH_SEPARATOR=':'
SHELL='/bin/sh'
SOEXT=''
STATIC_LIBS='-ldl '
ac_ct_CC='cc'
ac_ct_CXX=''
ac_ct_FC='ifort'
bindir='${exec_prefix}/bin'
build_alias=''
build_dir=''
datadir='${datarootdir}'
datarootdir='${prefix}/share'
disable_dependency_tracking=''
docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
dot=''
doxygen=''
dvidir='${docdir}'
exec_prefix='NONE'
host_alias=''
htmldir='${docdir}'
includedir='${prefix}/include'
infodir='${datarootdir}/info'
libdir='${exec_prefix}/lib'
libexecdir='${exec_prefix}/libexec'
localedir='${datarootdir}/locale'
localstatedir='${prefix}/var'
make_doc=''
make_pdfdoc=''
mandir='${datarootdir}/man'
oldincludedir='/usr/include'
pdfdir='${docdir}'
prefix='/global/homes/s/smarks/programs/knl/plumed/2.2.2/hrex/mpi/shared'
program_can_run=''
program_can_run_mpi=''
program_name=''
program_transform_name='s,x,x,'
psdir='${docdir}'
sbindir='${exec_prefix}/sbin'
sharedstatedir='${prefix}/com'
sysconfdir='${prefix}/etc'
target_alias=''
xxd=''

## ----------- ##
## confdefs.h. ##
## ----------- ##

/* confdefs.h */
#define PACKAGE_NAME "PLUMED"
#define PACKAGE_TARNAME "plumed"
#define PACKAGE_VERSION "2"
#define PACKAGE_STRING "PLUMED 2"
#define PACKAGE_BUGREPORT ""
#define PACKAGE_URL ""
#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 __PLUMED_HAS_EXTERNAL_BLAS 1
#define __PLUMED_HAS_EXTERNAL_LAPACK 1
#define __PLUMED_HAS_MOLFILE_PLUGINS 1
#define __PLUMED_HAS_MPI 1

configure: caught signal 15
configure: exit 1

Any assistance in resolving the issue is greatly appreciated. Thanks in advance!

Sean

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Sean Marks

unread,
Oct 3, 2017, 1:49:04 PM10/3/17
to PLUMED users
Hi, Giovanni,

Yes, I realized I made a silly mistake and tried to delete the post. Sorry for the hassle. I will also switch over to PLUMED 2.3 as you suggest; I didn't realize that it had the HREX changes built in, which is awesome.

If I run into any real issues with PLUMED 2.3, I will make a new thread.

Sincerely,

Sean
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