"make pflotran" fails: cannot find .mod files
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Jay Hendren
Apr 29, 2014, 5:07:29 PM4/29/14
to pflotr...@googlegroups.com
I'm building petsc-dev and pflotran-dev on the following platform:
[bechtel ~]% cat /etc/redhat-release
Red Hat Enterprise Linux Client release 5.10 (Tikanga)
[bechtel ~]% uname -r
2.6.18-371.6.1.el5
[bechtel ~]% gfortran --version
GNU Fortran (GCC) 4.7.2
Copyright (C) 2012 Free Software Foundation, Inc.
I built petsc-dev with the following:
[bechtel ~/petsc]% ./configure --download-mpich=yes --download-hdf5=yes --download-fblaslapack=yes
Configure and make completed successfully, as did the test:
[bechtel ~/petsc]% make test
Running test examples to verify correct installation
Using PETSC_DIR=/data/home/systems/hendrenj/petsc and PETSC_ARCH=arch-linux2-c-debug
C/C++ example src/snes/examples/tutorials/ex19 run successfully with 1 MPI process
C/C++ example src/snes/examples/tutorials/ex19 run successfully with 2 MPI processes
Fortran example src/snes/examples/tutorials/ex5f run successfully with 1 MPI process
Completed test examples
=========================================
Now to evaluate the computer systems you plan use - do:
make PETSC_DIR=/data/home/systems/hendrenj/petsc PETSC_ARCH=arch-linux2-c-debug streams NPMAX=<number of MPI processes you intend to use>
Here is the commit I am using in my copy of petsc-dev:
[bechtel ~/petsc]% git log -1 HEAD
commit 0c8c14c502e79aaeb7ec26e1cd1e476322d9010e
Author: Barry Smith <bsm...@mcs.anl.gov>
Date: Wed Apr 16 13:56:11 2014 -0500
double http:// in message
Reported-by: "Jose E. Roman" <jro...@dsic.upv.es>
I made sure to set my environment variables before running "make pflotran":
[bechtel ~/pflotran-dev/src/pflotran]% export PETSC_DIR=/data/home/systems/hendrenj/petsc
[bechtel ~/pflotran-dev/src/pflotran]% export PETSC_ARCH=arch-linux2-c-debug
I used the following clean checkout of pflotran:
[bechtel ~/pflotran-dev/src/pflotran]% hg parent
changeset: 7590:ca0f051e7274
tag: tip
user: Gautam Bisht <gbi...@lbl.gov>
date: Tue Apr 22 12:06:30 2014 -0700
summary: made specific heat capacity of ice and water equal for surface-flow in TH mode.
[bechtel ~/pflotran-dev/src/pflotran]% hg status -q
[bechtel ~/pflotran-dev/src/pflotran]%
Then I attempted to compile:
[bechtel ~/pflotran-dev/src/pflotran]% make pflotran
This resulted in a variety of errors. Here are the first few errors,
along with some context:
/data/home/systems/hendrenj/petsc/arch-linux2-c-debug/bin/mpif90 -c -fPIC -Wall -Wno-unused-variable -Wno-unused-dummy-argument -g -O0 -I/data/home/systems/hendrenj/petsc/include -I/data/home/systems/hendrenj/petsc/arch-linux2-c-debug/include -I. -DPROCESS_MODEL -DCHUAN_CO2 -DGEOMECH -o dataset_base.o dataset_base.F90
/data/home/systems/hendrenj/petsc/arch-linux2-c-debug/bin/mpif90 -c -fPIC -Wall -Wno-unused-variable -Wno-unused-dummy-argument -g -O0 -I/data/home/systems/hendrenj/petsc/include -I/data/home/systems/hendrenj/petsc/arch-linux2-c-debug/include -I. -DPROCESS_MODEL -DCHUAN_CO2 -DGEOMECH -o hdf5_aux.o hdf5_aux.F90
hdf5_aux.F90:61.6:
use hdf5
1
Fatal Error: Parse error when checking module version for file 'hdf5.mod' opened at (1)
make: [hdf5_aux.o] Error 1 (ignored)
/data/home/systems/hendrenj/petsc/arch-linux2-c-debug/bin/mpif90 -c -fPIC -Wall -Wno-unused-variable -Wno-unused-dummy-argument -g -O0 -I/data/home/systems/hendrenj/petsc/include -I/data/home/systems/hendrenj/petsc/arch-linux2-c-debug/include -I. -DPROCESS_MODEL -DCHUAN_CO2 -DGEOMECH -o dataset_common_hdf5.o dataset_common_hdf5.F90
dataset_common_hdf5.F90:240.6:
use hdf5
1
Fatal Error: Parse error when checking module version for file 'hdf5.mod' opened at (1)
make: [dataset_common_hdf5.o] Error 1 (ignored)
/data/home/systems/hendrenj/petsc/arch-linux2-c-debug/bin/mpif90 -c -fPIC -Wall -Wno-unused-variable -Wno-unused-dummy-argument -g -O0 -I/data/home/systems/hendrenj/petsc/include -I/data/home/systems/hendrenj/petsc/arch-linux2-c-debug/include -I. -DPROCESS_MODEL -DCHUAN_CO2 -DGEOMECH -o material_aux.o material_aux.F90
/data/home/systems/hendrenj/petsc/arch-linux2-c-debug/bin/mpif90 -c -fPIC -Wall -Wno-unused-variable -Wno-unused-dummy-argument -g -O0 -I/data/home/systems/hendrenj/petsc/include -I/data/home/systems/hendrenj/petsc/arch-linux2-c-debug/include -I. -DPROCESS_MODEL -DCHUAN_CO2 -DGEOMECH -o saturation_function.o saturation_function.F90
/data/home/systems/hendrenj/petsc/arch-linux2-c-debug/bin/mpif90 -c -fPIC -Wall -Wno-unused-variable -Wno-unused-dummy-argument -g -O0 -I/data/home/systems/hendrenj/petsc/include -I/data/home/systems/hendrenj/petsc/arch-linux2-c-debug/include -I. -DPROCESS_MODEL -DCHUAN_CO2 -DGEOMECH -o material.o material.F90
material.F90:3.6:
use Dataset_Common_HDF5_class
1
Fatal Error: Can't open module file 'dataset_common_hdf5_class.mod' for reading at (1): No such file or directory
make: [material.o] Error 1 (ignored)
/data/home/systems/hendrenj/petsc/arch-linux2-c-debug/bin/mpif90 -c -fPIC -Wall -Wno-unused-variable -Wno-unused-dummy-argument -g -O0 -I/data/home/systems/hendrenj/petsc/include -I/data/home/systems/hendrenj/petsc/arch-linux2-c-debug/include -I. -DPROCESS_MODEL -DCHUAN_CO2 -DGEOMECH -o mphase_pckr_mod.o mphase_pckr_mod.F90
mphase_pckr_mod.F90:3.6:
use Material_module
1
Fatal Error: Can't open module file 'material_module.mod' for reading at (1): No such file or directory
make: [mphase_pckr_mod.o] Error 1 (ignored)
I'm baffled as to why the some of these module files cannot be found -
they exist in locations specified with "-I" flags to gfortran. Some of
the other missing .mod files appear to be totally non-existent or not
yet compiled. Of coures, without these modules, make tries to soldier
on but ultimately fails:
gfortran: error: ./auxiliary.o: No such file or directory
gfortran: error: ./flash2_aux.o: No such file or directory
gfortran: error: ./immis_aux.o: No such file or directory
gfortran: error: ./mphase_aux.o: No such file or directory
gfortran: error: ./pm_base.o: No such file or directory
gfortran: error: ./pm_general.o: No such file or directory
gfortran: error: ./pm_flash2.o: No such file or directory
.
.
.
<snip>
.
.
.
gfortran: error: ./surface_flow.o: No such file or directory
gfortran: error: ./surface_init.o: No such file or directory
gfortran: error: ./surface_global.o: No such file or directory
gfortran: error: ./surface_realization.o: No such file or directory
gfortran: error: ./surface_simulation.o: No such file or directory
gfortran: error: ./surfsubsurface_simulation.o: No such file or directory
gfortran: error: ./surface_th.o: No such file or directory
gfortran: error: ./pflotran.o: No such file or directory
make: *** [pflotran] Error 1
Any assistance in resolving this issue would be greatly appreciated.
Regards,
Jay Hendren
[bechtel ~]% cat /etc/redhat-release
Red Hat Enterprise Linux Client release 5.10 (Tikanga)
[bechtel ~]% uname -r
2.6.18-371.6.1.el5
[bechtel ~]% gfortran --version
GNU Fortran (GCC) 4.7.2
Copyright (C) 2012 Free Software Foundation, Inc.
I built petsc-dev with the following:
[bechtel ~/petsc]% ./configure --download-mpich=yes --download-hdf5=yes --download-fblaslapack=yes
Configure and make completed successfully, as did the test:
[bechtel ~/petsc]% make test
Running test examples to verify correct installation
Using PETSC_DIR=/data/home/systems/hendrenj/petsc and PETSC_ARCH=arch-linux2-c-debug
C/C++ example src/snes/examples/tutorials/ex19 run successfully with 1 MPI process
C/C++ example src/snes/examples/tutorials/ex19 run successfully with 2 MPI processes
Fortran example src/snes/examples/tutorials/ex5f run successfully with 1 MPI process
Completed test examples
=========================================
Now to evaluate the computer systems you plan use - do:
make PETSC_DIR=/data/home/systems/hendrenj/petsc PETSC_ARCH=arch-linux2-c-debug streams NPMAX=<number of MPI processes you intend to use>
Here is the commit I am using in my copy of petsc-dev:
[bechtel ~/petsc]% git log -1 HEAD
commit 0c8c14c502e79aaeb7ec26e1cd1e476322d9010e
Author: Barry Smith <bsm...@mcs.anl.gov>
Date: Wed Apr 16 13:56:11 2014 -0500
double http:// in message
Reported-by: "Jose E. Roman" <jro...@dsic.upv.es>
I made sure to set my environment variables before running "make pflotran":
[bechtel ~/pflotran-dev/src/pflotran]% export PETSC_DIR=/data/home/systems/hendrenj/petsc
[bechtel ~/pflotran-dev/src/pflotran]% export PETSC_ARCH=arch-linux2-c-debug
I used the following clean checkout of pflotran:
[bechtel ~/pflotran-dev/src/pflotran]% hg parent
changeset: 7590:ca0f051e7274
tag: tip
user: Gautam Bisht <gbi...@lbl.gov>
date: Tue Apr 22 12:06:30 2014 -0700
summary: made specific heat capacity of ice and water equal for surface-flow in TH mode.
[bechtel ~/pflotran-dev/src/pflotran]% hg status -q
[bechtel ~/pflotran-dev/src/pflotran]%
Then I attempted to compile:
[bechtel ~/pflotran-dev/src/pflotran]% make pflotran
This resulted in a variety of errors. Here are the first few errors,
along with some context:
/data/home/systems/hendrenj/petsc/arch-linux2-c-debug/bin/mpif90 -c -fPIC -Wall -Wno-unused-variable -Wno-unused-dummy-argument -g -O0 -I/data/home/systems/hendrenj/petsc/include -I/data/home/systems/hendrenj/petsc/arch-linux2-c-debug/include -I. -DPROCESS_MODEL -DCHUAN_CO2 -DGEOMECH -o dataset_base.o dataset_base.F90
/data/home/systems/hendrenj/petsc/arch-linux2-c-debug/bin/mpif90 -c -fPIC -Wall -Wno-unused-variable -Wno-unused-dummy-argument -g -O0 -I/data/home/systems/hendrenj/petsc/include -I/data/home/systems/hendrenj/petsc/arch-linux2-c-debug/include -I. -DPROCESS_MODEL -DCHUAN_CO2 -DGEOMECH -o hdf5_aux.o hdf5_aux.F90
hdf5_aux.F90:61.6:
use hdf5
1
Fatal Error: Parse error when checking module version for file 'hdf5.mod' opened at (1)
make: [hdf5_aux.o] Error 1 (ignored)
/data/home/systems/hendrenj/petsc/arch-linux2-c-debug/bin/mpif90 -c -fPIC -Wall -Wno-unused-variable -Wno-unused-dummy-argument -g -O0 -I/data/home/systems/hendrenj/petsc/include -I/data/home/systems/hendrenj/petsc/arch-linux2-c-debug/include -I. -DPROCESS_MODEL -DCHUAN_CO2 -DGEOMECH -o dataset_common_hdf5.o dataset_common_hdf5.F90
dataset_common_hdf5.F90:240.6:
use hdf5
1
Fatal Error: Parse error when checking module version for file 'hdf5.mod' opened at (1)
make: [dataset_common_hdf5.o] Error 1 (ignored)
/data/home/systems/hendrenj/petsc/arch-linux2-c-debug/bin/mpif90 -c -fPIC -Wall -Wno-unused-variable -Wno-unused-dummy-argument -g -O0 -I/data/home/systems/hendrenj/petsc/include -I/data/home/systems/hendrenj/petsc/arch-linux2-c-debug/include -I. -DPROCESS_MODEL -DCHUAN_CO2 -DGEOMECH -o material_aux.o material_aux.F90
/data/home/systems/hendrenj/petsc/arch-linux2-c-debug/bin/mpif90 -c -fPIC -Wall -Wno-unused-variable -Wno-unused-dummy-argument -g -O0 -I/data/home/systems/hendrenj/petsc/include -I/data/home/systems/hendrenj/petsc/arch-linux2-c-debug/include -I. -DPROCESS_MODEL -DCHUAN_CO2 -DGEOMECH -o saturation_function.o saturation_function.F90
/data/home/systems/hendrenj/petsc/arch-linux2-c-debug/bin/mpif90 -c -fPIC -Wall -Wno-unused-variable -Wno-unused-dummy-argument -g -O0 -I/data/home/systems/hendrenj/petsc/include -I/data/home/systems/hendrenj/petsc/arch-linux2-c-debug/include -I. -DPROCESS_MODEL -DCHUAN_CO2 -DGEOMECH -o material.o material.F90
material.F90:3.6:
use Dataset_Common_HDF5_class
1
Fatal Error: Can't open module file 'dataset_common_hdf5_class.mod' for reading at (1): No such file or directory
make: [material.o] Error 1 (ignored)
/data/home/systems/hendrenj/petsc/arch-linux2-c-debug/bin/mpif90 -c -fPIC -Wall -Wno-unused-variable -Wno-unused-dummy-argument -g -O0 -I/data/home/systems/hendrenj/petsc/include -I/data/home/systems/hendrenj/petsc/arch-linux2-c-debug/include -I. -DPROCESS_MODEL -DCHUAN_CO2 -DGEOMECH -o mphase_pckr_mod.o mphase_pckr_mod.F90
mphase_pckr_mod.F90:3.6:
use Material_module
1
Fatal Error: Can't open module file 'material_module.mod' for reading at (1): No such file or directory
make: [mphase_pckr_mod.o] Error 1 (ignored)
I'm baffled as to why the some of these module files cannot be found -
they exist in locations specified with "-I" flags to gfortran. Some of
the other missing .mod files appear to be totally non-existent or not
yet compiled. Of coures, without these modules, make tries to soldier
on but ultimately fails:
gfortran: error: ./auxiliary.o: No such file or directory
gfortran: error: ./flash2_aux.o: No such file or directory
gfortran: error: ./immis_aux.o: No such file or directory
gfortran: error: ./mphase_aux.o: No such file or directory
gfortran: error: ./pm_base.o: No such file or directory
gfortran: error: ./pm_general.o: No such file or directory
gfortran: error: ./pm_flash2.o: No such file or directory
.
.
.
<snip>
.
.
.
gfortran: error: ./surface_flow.o: No such file or directory
gfortran: error: ./surface_init.o: No such file or directory
gfortran: error: ./surface_global.o: No such file or directory
gfortran: error: ./surface_realization.o: No such file or directory
gfortran: error: ./surface_simulation.o: No such file or directory
gfortran: error: ./surfsubsurface_simulation.o: No such file or directory
gfortran: error: ./surface_th.o: No such file or directory
gfortran: error: ./pflotran.o: No such file or directory
make: *** [pflotran] Error 1
Any assistance in resolving this issue would be greatly appreciated.
Regards,
Jay Hendren
Hammond, Glenn E
Apr 29, 2014, 5:31:59 PM4/29/14
to pflotr...@googlegroups.com
Please send $PETSC_DIR/$PETSC_ARCH/conf/configure.log
Glenn
> --
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> https://groups.google.com/d/msgid/pflotran-
> dev/201404292107.s3TL7T5l017549%40refuge.colorado.edu.
Glenn
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> https://groups.google.com/d/msgid/pflotran-
> dev/201404292107.s3TL7T5l017549%40refuge.colorado.edu.
Hammond, Glenn E
Apr 29, 2014, 7:52:21 PM4/29/14
to pflotr...@googlegroups.com
hdf5.mod is not being found. I pulled the latest petsc-dev and PFLOTRAN compiles against it properly.
A couple questions:
1. Is 'hdf5.mod' found in $PETSC_DIR/$PETSC_ARCH/include? Try 'ls $PETSC_DIR/$PETSC_ARCH/include/hdf5.mod'.
2. Have you successfully built PFLOTRAN in the past?
3. Please send a complete make.log for PFLOTRAN. I.e. 'make pflotran >& make.log'
Glenn
> -----Original Message-----
> From: pflotr...@googlegroups.com [mailto:pflotran-
> d...@googlegroups.com] On Behalf Of Jay Hendren
> Sent: Tuesday, April 29, 2014 2:07 PM
> To: pflotr...@googlegroups.com
> Subject: [EXTERNAL] [pflotran-dev: 1904] "make pflotran" fails: cannot find
> .mod files
>
A couple questions:
1. Is 'hdf5.mod' found in $PETSC_DIR/$PETSC_ARCH/include? Try 'ls $PETSC_DIR/$PETSC_ARCH/include/hdf5.mod'.
2. Have you successfully built PFLOTRAN in the past?
3. Please send a complete make.log for PFLOTRAN. I.e. 'make pflotran >& make.log'
Glenn
> -----Original Message-----
> From: pflotr...@googlegroups.com [mailto:pflotran-
> d...@googlegroups.com] On Behalf Of Jay Hendren
> Sent: Tuesday, April 29, 2014 2:07 PM
> To: pflotr...@googlegroups.com
> Subject: [EXTERNAL] [pflotran-dev: 1904] "make pflotran" fails: cannot find
> .mod files
>
> -fPIC -Wall -Wno-unused-variable -Wno-unused-dummy-argument -g -O0 -
> I/data/home/systems/hendrenj/petsc/include -
> I/data/home/systems/hendrenj/petsc/arch-linux2-c-debug/include -I. -
> I/data/home/systems/hendrenj/petsc/include -
> I/data/home/systems/hendrenj/petsc/arch-linux2-c-debug/include -I. -
> DPROCESS_MODEL -DCHUAN_CO2 -DGEOMECH -o dataset_base.o
> dataset_base.F90
> /data/home/systems/hendrenj/petsc/arch-linux2-c-debug/bin/mpif90 -c
> dataset_base.F90
> /data/home/systems/hendrenj/petsc/arch-linux2-c-debug/bin/mpif90 -c
> -fPIC -Wall -Wno-unused-variable -Wno-unused-dummy-argument -g -O0 -
> I/data/home/systems/hendrenj/petsc/include -
> I/data/home/systems/hendrenj/petsc/arch-linux2-c-debug/include -I. -
> I/data/home/systems/hendrenj/petsc/include -
> I/data/home/systems/hendrenj/petsc/arch-linux2-c-debug/include -I. -
> DPROCESS_MODEL -DCHUAN_CO2 -DGEOMECH -o hdf5_aux.o hdf5_aux.F90
> hdf5_aux.F90:61.6:
>
> use hdf5
> 1
> Fatal Error: Parse error when checking module version for file 'hdf5.mod'
> opened at (1)
> make: [hdf5_aux.o] Error 1 (ignored)
> /data/home/systems/hendrenj/petsc/arch-linux2-c-debug/bin/mpif90 -c
> hdf5_aux.F90:61.6:
>
> use hdf5
> 1
> Fatal Error: Parse error when checking module version for file 'hdf5.mod'
> opened at (1)
> make: [hdf5_aux.o] Error 1 (ignored)
> /data/home/systems/hendrenj/petsc/arch-linux2-c-debug/bin/mpif90 -c
> -fPIC -Wall -Wno-unused-variable -Wno-unused-dummy-argument -g -O0 -
> I/data/home/systems/hendrenj/petsc/include -
> I/data/home/systems/hendrenj/petsc/arch-linux2-c-debug/include -I. -
> I/data/home/systems/hendrenj/petsc/include -
> I/data/home/systems/hendrenj/petsc/arch-linux2-c-debug/include -I. -
> DPROCESS_MODEL -DCHUAN_CO2 -DGEOMECH -o dataset_common_hdf5.o
> dataset_common_hdf5.F90
> dataset_common_hdf5.F90:240.6:
>
> use hdf5
> 1
> Fatal Error: Parse error when checking module version for file 'hdf5.mod'
> opened at (1)
> make: [dataset_common_hdf5.o] Error 1 (ignored)
> /data/home/systems/hendrenj/petsc/arch-linux2-c-debug/bin/mpif90 -c
> dataset_common_hdf5.F90
> dataset_common_hdf5.F90:240.6:
>
> use hdf5
> 1
> Fatal Error: Parse error when checking module version for file 'hdf5.mod'
> opened at (1)
> make: [dataset_common_hdf5.o] Error 1 (ignored)
> /data/home/systems/hendrenj/petsc/arch-linux2-c-debug/bin/mpif90 -c
> -fPIC -Wall -Wno-unused-variable -Wno-unused-dummy-argument -g -O0 -
> I/data/home/systems/hendrenj/petsc/include -
> I/data/home/systems/hendrenj/petsc/arch-linux2-c-debug/include -I. -
> I/data/home/systems/hendrenj/petsc/include -
> I/data/home/systems/hendrenj/petsc/arch-linux2-c-debug/include -I. -
> DPROCESS_MODEL -DCHUAN_CO2 -DGEOMECH -o material_aux.o
> material_aux.F90
> /data/home/systems/hendrenj/petsc/arch-linux2-c-debug/bin/mpif90 -c
> material_aux.F90
> /data/home/systems/hendrenj/petsc/arch-linux2-c-debug/bin/mpif90 -c
> -fPIC -Wall -Wno-unused-variable -Wno-unused-dummy-argument -g -O0 -
> I/data/home/systems/hendrenj/petsc/include -
> I/data/home/systems/hendrenj/petsc/arch-linux2-c-debug/include -I. -
> I/data/home/systems/hendrenj/petsc/include -
> I/data/home/systems/hendrenj/petsc/arch-linux2-c-debug/include -I. -
> DPROCESS_MODEL -DCHUAN_CO2 -DGEOMECH -o saturation_function.o
> saturation_function.F90
> /data/home/systems/hendrenj/petsc/arch-linux2-c-debug/bin/mpif90 -c
> saturation_function.F90
> /data/home/systems/hendrenj/petsc/arch-linux2-c-debug/bin/mpif90 -c
> -fPIC -Wall -Wno-unused-variable -Wno-unused-dummy-argument -g -O0 -
> I/data/home/systems/hendrenj/petsc/include -
> I/data/home/systems/hendrenj/petsc/arch-linux2-c-debug/include -I. -
> I/data/home/systems/hendrenj/petsc/include -
> I/data/home/systems/hendrenj/petsc/arch-linux2-c-debug/include -I. -
> DPROCESS_MODEL -DCHUAN_CO2 -DGEOMECH -o material.o material.F90
> material.F90:3.6:
>
> use Dataset_Common_HDF5_class
> 1
> Fatal Error: Can't open module file 'dataset_common_hdf5_class.mod' for
> reading at (1): No such file or directory
> make: [material.o] Error 1 (ignored)
> /data/home/systems/hendrenj/petsc/arch-linux2-c-debug/bin/mpif90 -c
> material.F90:3.6:
>
> use Dataset_Common_HDF5_class
> 1
> Fatal Error: Can't open module file 'dataset_common_hdf5_class.mod' for
> reading at (1): No such file or directory
> make: [material.o] Error 1 (ignored)
> /data/home/systems/hendrenj/petsc/arch-linux2-c-debug/bin/mpif90 -c
> -fPIC -Wall -Wno-unused-variable -Wno-unused-dummy-argument -g -O0 -
> I/data/home/systems/hendrenj/petsc/include -
> I/data/home/systems/hendrenj/petsc/arch-linux2-c-debug/include -I. -
> I/data/home/systems/hendrenj/petsc/include -
> I/data/home/systems/hendrenj/petsc/arch-linux2-c-debug/include -I. -
Jay Hendren
Apr 29, 2014, 9:34:34 PM4/29/14
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1. Yes, the .mod files are there:
[bechtel ~]% ls petsc/arch-linux2-c-debug/include
H5ACpublic.h h5f.mod H5Rpublic.h petscconfiginfo.h
h5a.mod h5fortran_types.mod h5s.mod petscdef.mod
H5api_adpt.h H5Fpublic.h H5Spublic.h petscdmcomposite.mod
h5a_provisional.mod h5global.mod h5tb.mod petscdmdadef.mod
H5Apublic.h h5g.mod H5TBpublic.h petscdmda.mod
H5Cpublic.h H5Gpublic.h h5t.mod petscdmdef.mod
h5_dble_interface.mod h5im.mod h5t_provisional.mod petscdm.mod
h5d.mod h5i.mod H5Tpublic.h petscfix.h
h5d_provisional.mod H5IMpublic.h H5version.h petscisdef.mod
H5Dpublic.h H5Ipublic.h h5z.mod petscis.mod
h5ds.mod h5lib.mod H5Zpublic.h petsckspdef.mod
H5DSpublic.h h5lib_provisional.mod hdf5.h petscksp.mod
h5e.mod h5l.mod hdf5_hl.h petscmachineinfo.h
h5e_provisional.mod h5l_provisional.mod hdf5.mod petscmatdef.mod
H5Epubgen.h H5Lpublic.h mpi_base.mod petscmat.mod
H5Epublic.h h5lt.mod mpi_constants.mod petsc.mod
H5f90i_gen.h H5LTpublic.h mpicxx.h petscpcdef.mod
H5f90i.h H5MMpublic.h mpif.h petscpc.mod
H5FDcore.h h5o.mod mpi.h petscsnesdef.mod
H5FDdirect.h h5o_provisional.mod mpi.mod petscsnes.mod
H5FDfamily.h H5Opublic.h mpiof.h petscsysdef.mod
H5FDlog.h H5overflow.h mpio.h petscsys.mod
H5FDmpi.h h5p.mod mpi_sizeofs.mod petsctsdef.mod
H5FDmpio.h h5p_provisional.mod opa_config.h petscts.mod
h5fdmpio.mod H5Ppublic.h opa_primitives.h petscvecdef.mod
H5FDmpiposix.h H5PTpublic.h opa_queue.h petscvec.mod
H5FDmulti.h H5pubconf.h opa_util.h primitives/
H5FDpublic.h H5public.h petscaodef.mod
H5FDsec2.h h5r.mod petscao.mod
H5FDstdio.h h5r_provisional.mod petscconf.h
2. No, I have never built pflotran before. pflotran has been successfully installed on this system in the past, but it was through a packaged distribution and not built from source.
3. attached. The first error occurs around line 85.
[bechtel ~]% ls petsc/arch-linux2-c-debug/include
H5ACpublic.h h5f.mod H5Rpublic.h petscconfiginfo.h
h5a.mod h5fortran_types.mod h5s.mod petscdef.mod
H5api_adpt.h H5Fpublic.h H5Spublic.h petscdmcomposite.mod
h5a_provisional.mod h5global.mod h5tb.mod petscdmdadef.mod
H5Apublic.h h5g.mod H5TBpublic.h petscdmda.mod
H5Cpublic.h H5Gpublic.h h5t.mod petscdmdef.mod
h5_dble_interface.mod h5im.mod h5t_provisional.mod petscdm.mod
h5d.mod h5i.mod H5Tpublic.h petscfix.h
h5d_provisional.mod H5IMpublic.h H5version.h petscisdef.mod
H5Dpublic.h H5Ipublic.h h5z.mod petscis.mod
h5ds.mod h5lib.mod H5Zpublic.h petsckspdef.mod
H5DSpublic.h h5lib_provisional.mod hdf5.h petscksp.mod
h5e.mod h5l.mod hdf5_hl.h petscmachineinfo.h
h5e_provisional.mod h5l_provisional.mod hdf5.mod petscmatdef.mod
H5Epubgen.h H5Lpublic.h mpi_base.mod petscmat.mod
H5Epublic.h h5lt.mod mpi_constants.mod petsc.mod
H5f90i_gen.h H5LTpublic.h mpicxx.h petscpcdef.mod
H5f90i.h H5MMpublic.h mpif.h petscpc.mod
H5FDcore.h h5o.mod mpi.h petscsnesdef.mod
H5FDdirect.h h5o_provisional.mod mpi.mod petscsnes.mod
H5FDfamily.h H5Opublic.h mpiof.h petscsysdef.mod
H5FDlog.h H5overflow.h mpio.h petscsys.mod
H5FDmpi.h h5p.mod mpi_sizeofs.mod petsctsdef.mod
H5FDmpio.h h5p_provisional.mod opa_config.h petscts.mod
h5fdmpio.mod H5Ppublic.h opa_primitives.h petscvecdef.mod
H5FDmpiposix.h H5PTpublic.h opa_queue.h petscvec.mod
H5FDmulti.h H5pubconf.h opa_util.h primitives/
H5FDpublic.h H5public.h petscaodef.mod
H5FDsec2.h h5r.mod petscao.mod
H5FDstdio.h h5r_provisional.mod petscconf.h
2. No, I have never built pflotran before. pflotran has been successfully installed on this system in the past, but it was through a packaged distribution and not built from source.
3. attached. The first error occurs around line 85.
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