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King
Nov 9, 2015, 1:23:21 AM11/9/15
to OpenMC Users Group
Hello everyone.
I have run into problem while installing current develop branch. prior to current changes regarding hdf5 only output, i used these commands to install openmc with parallel hdf5
export FC=/opt/phdf5/1.8.15-gnu/bin/h5pfc
I have run into problem while installing current develop branch. prior to current changes regarding hdf5 only output, i used these commands to install openmc with parallel hdf5
export FC=/opt/phdf5/1.8.15-gnu/bin/h5pfc
cmake -H. -Bbuild
make -s -C build -j
now i installed parallel hdf5 version 1.8.15 in the path shown above. and set FC=h5pfc (bin directory of HDF5 placed in my path variable). i get this error
-- The Fortran compiler identification is GNU
-- Check for working Fortran compiler: /opt/phdf5/1.8.15-gnu/bin/h5pfc
-- Check for working Fortran compiler: /opt/phdf5/1.8.15-gnu/bin/h5pfc -- works
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Checking whether /opt/phdf5/1.8.15-gnu/bin/h5pfc supports Fortran 90
-- Checking whether /opt/phdf5/1.8.15-gnu/bin/h5pfc supports Fortran 90 -- yes
-- Found HDF5: /opt/phdf5/1.8.15-gnu/lib/libhdf5hl_fortran.so;/opt/phdf5/1.8.15-gnu/lib/libhdf5_hl.so;/opt/phdf5/1.8.15-gnu/lib/libhdf5_fortran.so;/opt/phdf5/1.8.15-gnu/lib/libhdf5.so;-ldl;-lm (found version "1.8.15")
CMake Error at CMakeLists.txt:78 (message):
Parallel HDF5 must be used with MPI.
-- Configuring incomplete, errors occurred!
See also "/home/osboxes/Work/openmc/build/CMakeFiles/CMakeOutput.log".
i have also tried using FC=mpif90. now the cmake executes successfully. output is given below
-- The Fortran compiler identification is GNU
-- Check for working Fortran compiler: /opt/mpich/3.1.3-gnu/bin/mpif90
-- Check for working Fortran compiler: /opt/mpich/3.1.3-gnu/bin/mpif90 -- works
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Checking whether /opt/mpich/3.1.3-gnu/bin/mpif90 supports Fortran 90
-- Checking whether /opt/mpich/3.1.3-gnu/bin/mpif90 supports Fortran 90 -- yes
-- Detected MPI wrapper: /opt/mpich/3.1.3-gnu/bin/mpif90
-- Found HDF5: /opt/phdf5/1.8.15-gnu/lib/libhdf5hl_fortran.so;/opt/phdf5/1.8.15-gnu/lib/libhdf5_hl.so;/opt/phdf5/1.8.15-gnu/lib/libhdf5_fortran.so;/opt/phdf5/1.8.15-gnu/lib/libhdf5.so;-ldl;-lm (found version "1.8.15")
-- Using parallel HDF5
-- Found PythonInterp: /usr/bin/python (found version "2.7.6")
-- Configuring done
-- Generating done
-- Build files have been written to: /home/osboxes/Work/openmc/build
then use the "make -s -C build -j" command. it runs successfully. then i use the "make install " which also happens successfully. but when i use "openmc --version" i get an error
openmc: error while loading shared libraries: libhdf5hl_fortran.so.10: cannot open shared object file: No such file or directory
can you please help me out with this. what i need to do to sort this error. and now should we use FC=mpif90??
make -s -C build -j
now i installed parallel hdf5 version 1.8.15 in the path shown above. and set FC=h5pfc (bin directory of HDF5 placed in my path variable). i get this error
-- The Fortran compiler identification is GNU
-- Check for working Fortran compiler: /opt/phdf5/1.8.15-gnu/bin/h5pfc
-- Check for working Fortran compiler: /opt/phdf5/1.8.15-gnu/bin/h5pfc -- works
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Checking whether /opt/phdf5/1.8.15-gnu/bin/h5pfc supports Fortran 90
-- Checking whether /opt/phdf5/1.8.15-gnu/bin/h5pfc supports Fortran 90 -- yes
-- Found HDF5: /opt/phdf5/1.8.15-gnu/lib/libhdf5hl_fortran.so;/opt/phdf5/1.8.15-gnu/lib/libhdf5_hl.so;/opt/phdf5/1.8.15-gnu/lib/libhdf5_fortran.so;/opt/phdf5/1.8.15-gnu/lib/libhdf5.so;-ldl;-lm (found version "1.8.15")
CMake Error at CMakeLists.txt:78 (message):
Parallel HDF5 must be used with MPI.
-- Configuring incomplete, errors occurred!
See also "/home/osboxes/Work/openmc/build/CMakeFiles/CMakeOutput.log".
i have also tried using FC=mpif90. now the cmake executes successfully. output is given below
-- The Fortran compiler identification is GNU
-- Check for working Fortran compiler: /opt/mpich/3.1.3-gnu/bin/mpif90
-- Check for working Fortran compiler: /opt/mpich/3.1.3-gnu/bin/mpif90 -- works
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Checking whether /opt/mpich/3.1.3-gnu/bin/mpif90 supports Fortran 90
-- Checking whether /opt/mpich/3.1.3-gnu/bin/mpif90 supports Fortran 90 -- yes
-- Detected MPI wrapper: /opt/mpich/3.1.3-gnu/bin/mpif90
-- Found HDF5: /opt/phdf5/1.8.15-gnu/lib/libhdf5hl_fortran.so;/opt/phdf5/1.8.15-gnu/lib/libhdf5_hl.so;/opt/phdf5/1.8.15-gnu/lib/libhdf5_fortran.so;/opt/phdf5/1.8.15-gnu/lib/libhdf5.so;-ldl;-lm (found version "1.8.15")
-- Using parallel HDF5
-- Found PythonInterp: /usr/bin/python (found version "2.7.6")
-- Configuring done
-- Generating done
-- Build files have been written to: /home/osboxes/Work/openmc/build
then use the "make -s -C build -j" command. it runs successfully. then i use the "make install " which also happens successfully. but when i use "openmc --version" i get an error
openmc: error while loading shared libraries: libhdf5hl_fortran.so.10: cannot open shared object file: No such file or directory
can you please help me out with this. what i need to do to sort this error. and now should we use FC=mpif90??
Paul Romano
Nov 9, 2015, 11:17:21 AM11/9/15
to King, OpenMC Users Group
Yes, in the upcoming release, if you are using MPI (whether in combination with parallel HDF5 or not), you should use FC=mpif90. CMake now handles finding HDF5 and setting the appropriate compiler/linker flags rather than relying on the h5fc/h5pfc wrappers.
As to the error you're receiving, you need to make sure that the library directory for HDF5 is on your LD_LIBRARY_PATH environment variable. So, adding the following to your profile should fix it (assuming you are using bash):
export LD_LIBRARY_PATH=/opt/phdf5/1.8.15-gnu/lib:$LD_LIBRARY_PATH
Best,
Paul
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King
Nov 10, 2015, 10:36:21 AM11/10/15
to OpenMC Users Group
Thanks Paul. I was not able to try it today. Will try it first thing tomorrow and let you know. Thanks for your help.
Derek Gaston
Nov 10, 2015, 11:47:35 AM11/10/15
to King, OpenMC Users Group
Paul,
Just a heads up that on the newest version of Mac OSX (El Capitan, 10.11) you can't count on DYLD_LIBRARY_PATH (the equivalent to LD_LIBRARY_PATH for OSX).
They have essentially removed it for security reasons.
Instead, you must use rpaths to embed the path to dynamic libraries into your application binary at compile time.
Basically: the time for LD_LIBRARY_PATH and DYLD_LIBRARY_PATH are at an end.
I haven't noticed any problems yet with OpenMC due to this, but your email here reminded me about it (we just struggled through this on my own project). So, just thought I would give you guys a heads up.
Derek
Just a heads up that on the newest version of Mac OSX (El Capitan, 10.11) you can't count on DYLD_LIBRARY_PATH (the equivalent to LD_LIBRARY_PATH for OSX).
They have essentially removed it for security reasons.
Instead, you must use rpaths to embed the path to dynamic libraries into your application binary at compile time.
Basically: the time for LD_LIBRARY_PATH and DYLD_LIBRARY_PATH are at an end.
I haven't noticed any problems yet with OpenMC due to this, but your email here reminded me about it (we just struggled through this on my own project). So, just thought I would give you guys a heads up.
Derek
On Tue, Nov 10, 2015 at 10:36 AM King <khurrum...@gmail.com> wrote:
Thanks Paul. I was not able to try it today. Will try it first thing tomorrow and let you know. Thanks for your help.
Paul Romano
Nov 10, 2015, 12:06:40 PM11/10/15
to Derek Gaston, King, OpenMC Users Group
Thanks for pointing that out, Derek! At least for the version of CMake that I am using, it looks like the HDF5 library directory is given as an rpath, so no LD_LIBRARY_PATH or DYLD_LIBRARY_PATH hacks should be necessary.
King- if you could try the following and give the output of the linker line, that might be helpful in figuring out what's going on in your case:
cmake -DCMAKE_VERBOSE_MAKEFILE=on sourcedir
make
King
Nov 10, 2015, 10:47:28 PM11/10/15
to OpenMC Users Group, frie...@gmail.com, khurrum...@gmail.com
Dear Paul,
It worked! using the LD_LIBRARY_PATH for HDF5 fixed the problem. the same solution had to be applied again for libmpifort.so.12 so had to add mpich/lib to LD_LIBRARY_PATH also. i am also placing the output of cmake -DCMAKE_VERBOSE_MAKEFILE=on here for reference
cmake -H. -Bbuild -DCMAKE_VERBOSE_MAKEFILE=on
It worked! using the LD_LIBRARY_PATH for HDF5 fixed the problem. the same solution had to be applied again for libmpifort.so.12 so had to add mpich/lib to LD_LIBRARY_PATH also. i am also placing the output of cmake -DCMAKE_VERBOSE_MAKEFILE=on here for reference
cmake -H. -Bbuild -DCMAKE_VERBOSE_MAKEFILE=on
-- The Fortran compiler identification is GNU
-- Check for working Fortran compiler: /opt/mpich/3.1.3-gnu/bin/mpif90
-- Check for working Fortran compiler: /opt/mpich/3.1.3-gnu/bin/mpif90 -- works
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Checking whether /opt/mpich/3.1.3-gnu/bin/mpif90 supports Fortran 90
-- Checking whether /opt/mpich/3.1.3-gnu/bin/mpif90 supports Fortran 90 -- yes
-- Detected MPI wrapper: /opt/mpich/3.1.3-gnu/bin/mpif90
-- Found HDF5: /opt/phdf5/1.8.15-gnu/lib/libhdf5hl_fortran.so;/opt/phdf5/1.8.15-gnu/lib/libhdf5_hl.so;/opt/phdf5/1.8.15-gnu/lib/libhdf5_fortran.so;/opt/phdf5/1.8.15-gnu/lib/libhdf5.so;-ldl;-lm (found version "1.8.15")
-- Using parallel HDF5
-- Found PythonInterp: /usr/bin/python (found version "2.7.6")
-- Configuring done
-- Generating done
-- Build files have been written to: /home/osboxes/Work/openmc/build
osboxes@osboxes:~/Work/openmc$ make -s -C build -j
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thanks for your help :-)
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Building Fortran object CMakeFiles/openmc.dir/src/main.F90.o
Linking Fortran executable bin/openmc
/opt/mpich/3.1.3-gnu/bin/mpif90 CMakeFiles/openmc.dir/src/input_xml.F90.o CMakeFiles/openmc.dir/src/ppmlib.F90.o CMakeFiles/openmc.dir/src/geometry_header.F90.o CMakeFiles/openmc.dir/src/tally_initialize.F90.o CMakeFiles/openmc.dir/src/source.F90.o CMakeFiles/openmc.dir/src/cmfd_data.F90.o CMakeFiles/openmc.dir/src/tracking.F90.o CMakeFiles/openmc.dir/src/plot_header.F90.o CMakeFiles/openmc.dir/src/ace.F90.o CMakeFiles/openmc.dir/src/cmfd_prod_operator.F90.o CMakeFiles/openmc.dir/src/set_header.F90.o CMakeFiles/openmc.dir/src/state_point.F90.o CMakeFiles/openmc.dir/src/interpolation.F90.o CMakeFiles/openmc.dir/src/geometry.F90.o CMakeFiles/openmc.dir/src/ace_header.F90.o CMakeFiles/openmc.dir/src/cross_section.F90.o CMakeFiles/openmc.dir/src/particle_restart.F90.o CMakeFiles/openmc.dir/src/material_header.F90.o CMakeFiles/openmc.dir/src/message_passing.F90.o CMakeFiles/openmc.dir/src/error.F90.o CMakeFiles/openmc.dir/src/dict_header.F90.o CMakeFiles/openmc.dir/src/endf.F90.o CMakeFiles/openmc.dir/src/doppler.F90.o CMakeFiles/openmc.dir/src/list_header.F90.o CMakeFiles/openmc.dir/src/eigenvalue.F90.o CMakeFiles/openmc.dir/src/trigger.F90.o CMakeFiles/openmc.dir/src/progress_header.F90.o CMakeFiles/openmc.dir/src/simulation.F90.o CMakeFiles/openmc.dir/src/particle_restart_write.F90.o CMakeFiles/openmc.dir/src/mesh.F90.o CMakeFiles/openmc.dir/src/physics.F90.o CMakeFiles/openmc.dir/src/cmfd_solver.F90.o CMakeFiles/openmc.dir/src/vector_header.F90.o CMakeFiles/openmc.dir/src/search.F90.o CMakeFiles/openmc.dir/src/particle_header.F90.o CMakeFiles/openmc.dir/src/main.F90.o CMakeFiles/openmc.dir/src/tally.F90.o CMakeFiles/openmc.dir/src/string.F90.o CMakeFiles/openmc.dir/src/finalize.F90.o CMakeFiles/openmc.dir/src/source_header.F90.o CMakeFiles/openmc.dir/src/surface_header.F90.o CMakeFiles/openmc.dir/src/endf_header.F90.o CMakeFiles/openmc.dir/src/xml_interface.F90.o CMakeFiles/openmc.dir/src/plot.F90.o CMakeFiles/openmc.dir/src/random_lcg.F90.o CMakeFiles/openmc.dir/src/timer_header.F90.o CMakeFiles/openmc.dir/src/constants.F90.o CMakeFiles/openmc.dir/src/fission.F90.o CMakeFiles/openmc.dir/src/math.F90.o CMakeFiles/openmc.dir/src/energy_grid.F90.o CMakeFiles/openmc.dir/src/initialize.F90.o CMakeFiles/openmc.dir/src/hdf5_interface.F90.o CMakeFiles/openmc.dir/src/global.F90.o CMakeFiles/openmc.dir/src/matrix_header.F90.o CMakeFiles/openmc.dir/src/mesh_header.F90.o CMakeFiles/openmc.dir/src/cmfd_loss_operator.F90.o CMakeFiles/openmc.dir/src/cmfd_input.F90.o CMakeFiles/openmc.dir/src/summary.F90.o CMakeFiles/openmc.dir/src/output.F90.o CMakeFiles/openmc.dir/src/trigger_header.F90.o CMakeFiles/openmc.dir/src/tally_header.F90.o CMakeFiles/openmc.dir/src/track_output.F90.o CMakeFiles/openmc.dir/src/cmfd_header.F90.o CMakeFiles/openmc.dir/src/bank_header.F90.o CMakeFiles/openmc.dir/src/cmfd_execute.F90.o CMakeFiles/openmc.dir/src/stl_vector.F90.o CMakeFiles/openmc.dir/src/xml/openmc_fox.F90.o -o bin/openmc -rdynamic -fopenmp -L/opt/phdf5/1.8.15-gnu/lib /opt/phdf5/1.8.15-gnu/lib/libhdf5hl_fortran.so /opt/phdf5/1.8.15-gnu/lib/libhdf5_hl.so /opt/phdf5/1.8.15-gnu/lib/libhdf5_fortran.so /opt/phdf5/1.8.15-gnu/lib/libhdf5.so -ldl -lm lib/libfox_dom.a lib/libfox_wxml.a lib/libfox_sax.a lib/libfox_common.a lib/libfox_utils.a lib/libfox_fsys.a -Wl,-rpath,/opt/phdf5/1.8.15-gnu/lib:
[100%] Built target openmc
thanks for your help :-)
Paul Romano
Nov 11, 2015, 9:24:35 AM11/11/15
to King, OpenMC Users Group, frie...@gmail.com
Glad to hear it worked, although now I'm even more confused because according to the output, the library directory should have been embedded in the executable so that you shouldn't have needed to set LD_LIBRARY_PATH. I believe mpif90 also uses rpath (at least for MPICH) so that nothing special should be needed at run-time.
One more request: can you run the following command on the openmc executable?
objdump -p build/bin/openmc | egrep 'RPATH|RUNPATH'
Thanks,
Paul
King
Nov 12, 2015, 11:48:10 PM11/12/15
to OpenMC Users Group, khurrum...@gmail.com, frie...@gmail.com
Hello Paul,
The output of the command is
RUNPATH /opt/phdf5/1.8.15-gnu/lib::/opt/mpich/3.1.3-gnu/lib
The output of the command is
RUNPATH /opt/phdf5/1.8.15-gnu/lib::/opt/mpich/3.1.3-gnu/lib
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