I know that this is not a main stream debian question but I have not been able to get any response from the Trilinos (sandia labs) mailing list. I am desparate.
I am running a Debian Buster KDE system and am trying to set up Elmer with Trilinos. In short, a setup for some heavy duty computer modeling. Because of several factors, I chose to download the latest source code from GitHub. The CMake file (without MPI support) worked fine and the make file ran fine. But when I included MPI into the CMake file, (see below) the CMake still ran fine.
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#!/bin/bash
# Set this to the root of your Trilinos source directory.
TRILINOS_PATH=/opt/trilinos/Trilinos
#
# You can invoke this shell script with additional command-line
# arguments. They will be passed directly to CMake.
#
EXTRA_ARGS=$@
#
# Each invocation of CMake caches the values of build options in
a
# CMakeCache.txt file. If you run CMake again without deleting
the
# CMakeCache.txt file, CMake won't notice any build options that
have
# changed, because it found their original values in the cache
file.
# Deleting the CMakeCache.txt file before invoking CMake will
insure
# that CMake learns about any build options you may have
changed.
# Experience will teach you when you may omit this step.
#
rm -f CMakeCache.txt
#
# Enable all primary stable Trilinos packages.
#
cmake \
-D CMAKE_INSTALL_PREFIX:FILEPATH="/opt/trilinos/build" \
-D CMAKE_BUILD_TYPE:STRING=RELEASE \
-D TPL_ENABLE_MPI:BOOL=ON \
-D MPI_BASE_DIR:FILEPATH="/usr/lib/x86_64-linux-gnu" \
-D MPI_EXEC:FILEPATH="/usr/bin/mpiexec" \
-D Trilinos_ENABLE_ALL_PACKAGES:BOOL=ON \
$EXTRA_ARGS \
$TRILINOS_PATH
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But when I tried to run make I got the following errors:
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[ 17%] Built target suplib
[ 21%] Built target plt[ 17%] Built target suplib
[ 21%] Built target plt
[ 21%] Linking CXX executable exo2mat
[ 21%] Linking CXX executable conjoin
[ 21%] Linking CXX executable epu
[ 21%] Linking CXX executable exodiff
/usr/bin/ld: ..//.usr.//binlibraries//ldexodus:/
libexodus.a.(.ex_utils.c.o//)usr:/. .undefined reference/
binlibraries/toexodus /symbollibexodus.a/
ld':(H5get_libversionex_utils.c.o@)@:HDF5_SERIAL_1.8.7 .
./'undefined
/usr ..//binreference /to ldsymbol:
'/H5get_libversion/@usr@/HDF5_SERIAL_1.8.7lib'/
x86_64/-usrlinux/-bingnu//ldlibhdf5_serial.so.103:: /error/
usradding/ libsymbols/:x86_64 -DSOlinux -missinggnu
/fromlibhdf5_serial.so.103 :command errorline
adding symbols: DSO missing from command line
collect2: error: ld returned 1 exit status
libraries/exoduscollect2: error: ld returned 1 exit status
/libexodus.a(ex_utils.c.o): undefined reference to symbol
'H5get_libversion@@HDF5_SERIAL_1.8.7'
/usr/bin/ld: //usr/lib/x86_64-linux-gnu/libhdf5_serial.so.103:
error adding symbols: DSO missing from command line
collect2: error: ld returned 1 exit status
make[2]: ***
[packages/seacas/applications/epu/CMakeFiles/epu.dir/build.make:148:
packages/seacas/applications/epu/epu] Error 1
make[2]: ***
[packages/seacas/applications/conjoin/CMakeFiles/conjoin.dir/build.make:133:
packages/seacas/applications/conjoin/conjoin] Error 1
make[1]: *** [CMakeFiles/Makefile2:11114:
packages/seacas/applications/epu/CMakeFiles/epu.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
make[1]: *** [CMakeFiles/Makefile2:10982:
packages/seacas/applications/conjoin/CMakeFiles/conjoin.dir/all]
Error 2
make[2]: ***
[packages/seacas/applications/exo2mat/CMakeFiles/exo2mat.dir/build.make:89:
packages/seacas/applications/exo2mat/exo2mat] Error 1
make[1]: *** [CMakeFiles/Makefile2:11171:
packages/seacas/applications/exo2mat/CMakeFiles/exo2mat.dir/all]
Error 2
/usr/bin/ld: ../../libraries/exodus/libexodus.a(ex_utils.c.o):
undefined reference to symbol
'H5get_libversion@@HDF5_SERIAL_1.8.7'
/usr/bin/ld: //usr/lib/x86_64-linux-gnu/libhdf5_serial.so.103:
error adding symbols: DSO missing from command line
collect2: error: ld returned 1 exit status
make[2]: ***
[packages/seacas/applications/exodiff/CMakeFiles/exodiff.dir/build.make:298:
packages/seacas/applications/exodiff/exodiff] Error 1
make[1]: *** [CMakeFiles/Makefile2:11228:
packages/seacas/applications/exodiff/CMakeFiles/exodiff.dir/all]
Error 2
make: *** [Makefile:163: all] Error 2
gary@ctech:/opt/trilinos/build$
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If anyone familiar with this software could help it will be sincerely appreciated.
Gary R