#602: Problem with thorn EOS_Omni --------------------------+------------------------------------------------- Reporter: Maxim Barkov | Type: defect Status: new | Priority: major Milestone: | Component: EinsteinToolkit thorn Version: ET_2011_05 | Keywords: --------------------------+------------------------------------------------- Hello,
I have tried to compile the ET on my local PC. Ubuntu 11.04 2xXenon using the next procedure: make test1-config make test1
my ~/.cactus/config is follow ###################################### CC = gcc CXX = g++ F90 = gfortran F77 = gfortran
MPI = OpenMPI MPI_LIBS = -lmpi MPI_LIB_DIRS = /usr/lib/ MPI_INC_DIRS = /usr/include/openmpi/ ############################################
After many outputs I get:
________________________________________________________________________ Checking status of thorn EOS_Omni ________________________________________________________________________ Preprocessing /home/bmv/utils/soft/develop/ET/Cactus/arrangements/EinsteinEOS/EOS_Omni/src/nuc_eos/readtable.F90 Compiling /home/bmv/utils/soft/develop/ET/Cactus/arrangements/EinsteinEOS/EOS_Omni/src/nuc_eos/readtable.F90 /home/bmv/utils/soft/develop/ET/Cactus/configs/test1/build/EOS_Omni/nuc_eos/readtable.f90:5.10:
use hdf5 1 Fatal Error: Can't open module file 'hdf5.mod' for reading at (1): No such file or directory make[3]: *** [readtable.F90.o] Error 1 make[2]: *** [nuc_eos/make.checked] Error 2 make[1]: *** [/home/bmv/utils/soft/develop/ET/Cactus/configs/test1/lib/libthorn_EOS_Omni.a] Error 2 make: *** [test1] Error 2
Could you help me to solve this problem? Best wishes, Maxim
#602: Problem with thorn EOS_Omni ------------------------------------+--------------------------------------- Reporter: Maxim Barkov | Owner: Type: defect | Status: new Priority: major | Milestone: Component: EinsteinToolkit thorn | Version: ET_2011_05 Resolution: | Keywords: ------------------------------------+---------------------------------------
Comment (by rhaas):
Hello Maxim,
EOS_Omni requires Fortran bindings to libhdf5 (libhdf5_fortran.so and .a) which some Linux distributions do no install by default. You also need to activate the thorn {{{ ExternalLibraries/HDF5 }}} in your thorn list. You must also make sure that hdf5.mod is in '''include''' path of the Fortran compiler (http://mpc.uci.edu/man/gfortran.html). If HDF5 is already active, try adding {{{ HDF5_DIR=BUILD }}} to you config file (/home/bmv/.cactus/config it seems). Lastly you should make sure that you use the same compiler (and version) to build Cactus that was used to compile libhdf5 (not an issue if you use BUILD).
Yours, Roland
#602: Problem with thorn EOS_Omni ------------------------------------+--------------------------------------- Reporter: Maxim Barkov | Owner: Type: defect | Status: new Priority: major | Milestone: Component: EinsteinToolkit thorn | Version: ET_2011_05 Resolution: | Keywords: ------------------------------------+---------------------------------------
Comment (by anonymous):
Thank you Roland,
I have modify /home/bmv/.cactus/config by adding HDF5 = yes HDF5_DIR=BUILD
HDF5 is in the throns list. .... EinsteinUtils/TGRtensor # TGRtensor ( ) [ ] { } ExternalLibraries/BLAS # BLAS ( ) [ ] { } ExternalLibraries/GSL # GSL ( ) [ ] { } ExternalLibraries/HDF5 # HDF5 ( ) [ ] { } ExternalLibraries/LAPACK # LAPACK ( ) [ ] { } ExternalLibraries/LORENE # LORENE ( ) [ ] { } ExternalLibraries/OpenSSL # OpenSSL ( ) [ ] { } ExternalLibraries/libjpeg # libjpeg ( ) [ ] { } ExternalLibraries/zlib # zlib ( ) [ ] { } ....
Unfortunately, the mistake still on it's place.
Preprocessing /home/bmv/utils/soft/develop/ET/Cactus/arrangements/EinsteinEOS/EOS_Omni/src/nuc_eos/readtable.F90 Compiling /home/bmv/utils/soft/develop/ET/Cactus/arrangements/EinsteinEOS/EOS_Omni/src/nuc_eos/readtable.F90 /home/bmv/utils/soft/develop/ET/Cactus/configs/test1/build/EOS_Omni/nuc_eos/readtable.f90:5.10:
use hdf5 1 Fatal Error: Can't open module file 'hdf5.mod' for reading at (1): No such file or directory make[3]: *** [readtable.F90.o] Error 1 make[2]: *** [nuc_eos/make.checked] Error 2 make[1]: *** [/home/bmv/utils/soft/develop/ET/Cactus/configs/test1/lib/libthorn_EOS_Omni.a] Error 2 make: *** [test1] Error 2
Is it possible to show for the compiler the path to hdf5.mod in such configuration? (hdf5.mod not exist in the Cactus folder)
Best wishes, Maxim
#602: Problem with thorn EOS_Omni ------------------------------------+--------------------------------------- Reporter: Maxim Barkov | Owner: Type: defect | Status: new Priority: major | Milestone: Component: EinsteinToolkit thorn | Version: ET_2011_05 Resolution: | Keywords: ------------------------------------+---------------------------------------
Comment (by rhaas):
Hello Maxim,
{{{ HDF5=yes }}} should no longer be used (in fact it should generate a warning). Though this should not give you the errors you see.
I would suggest doing a {{{make test1-realclean}}} to make sure everything is rebuild (the ExternalLibraries are a bit odd that way). You should then see some messages from HDF5 during the initial compilation phase (CST configure I believe is the technical term), which should end in something like {{{HDF5_LIBRARIES = hdf5 hdf5_fortran hdf5_cxx ...}}}. Otherwise I have had success by manually (really bad idea usually, but it worked) copying hdf5.mod into Cactus/configs/test1/scratch .
If it still fails after a realclean, would you mind attaching all output ie: {{{ make test1-realclean make test1-config options=~/.cactus/config &>test1.log make test1 >>test1.log 2>>test1.log }}}
#602: Problem with thorn EOS_Omni ------------------------------------+--------------------------------------- Reporter: Maxim Barkov | Owner: Type: defect | Status: new Priority: major | Milestone: Component: EinsteinToolkit thorn | Version: ET_2011_05 Resolution: | Keywords: ------------------------------------+---------------------------------------
Comment (by anonymous):
Thank you Roland,
I do make test1-realclean and remove HDF5=yes After that ET was compiled successfully.
Now I try to run mpirun np 16 exe/cactus_test1 par/static_tov.par
Best wishes, Maxim
#602: Problem with thorn EOS_Omni ------------------------------------+--------------------------------------- Reporter: Maxim Barkov | Owner: Type: defect | Status: closed Priority: major | Milestone: Component: EinsteinToolkit thorn | Version: ET_2011_05 Resolution: fixed | Keywords: ------------------------------------+--------------------------------------- Changes (by knarf):
* status: new => closed * resolution: => fixed
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