Aaditya,
is NERSC Cori a machine where the front-end node runs a different
processor/system than the compute nodes? If so, you're building a library for
the compute nodes, and the tests are also built for the compute nodes. But
you're trying to run the test executables on the front-end node -- which might
help explain the error you see.
Best
W.
On 10/22/20 7:52 PM, Aaditya Lakshmanan wrote:
Hi Everyone,
I have been trying to install deal.ii on the NERSC Cori System and after a
seemingly successful cmake and make install, make test yields failure for all
the tests setup. I briefly detail the procedure I followed and the outputs and
errors obtained.
As a pre-requisite I installed p4est using the setup script(with some
modifications) and petsc manually with the configure.py script and appropriate
settings. The following modules were loaded :
Currently Loaded Modulefiles:
1) modules/3.2.11.4 5) craype-network-aries 9)
PrgEnv-intel/6.0.5 13) valgrind/3.15.0
2) altd/2.0 6) craype/2.6.2 10)
craype-mic-knl 14) zlib/1.2.11
3) darshan/3.1.7 7) pmi/5.0.14 11)
cray-mpich/7.7.14 15) cmake/3.14.4
4) intel/19.0.3.199 8) atp/2.1.3 12)
craype-hugepages2M 16) cray-hdf5-parallel/1.10.5.2
After setting the environment variables P4EST_DIR, PETSC_DIR and PETSC_ARCH, I
compiled dealii-9.1.1 as follows :
*cmake -DCMAKE_SYSTEM_NAME=CrayLinuxEnvironment -DCMAKE_C_COMPILER=cc
-DCMAKE_CXX_COMPILER=CC -DCMAKE_Fortran_COMPILER=ftn -DDEAL_II_WITH_MPI=ON
-DDEAL_II_WITH_PETSC=ON -DDEAL_II_WITH_P4EST=ON -DDEAL_II_WITH_LAPACK=ON
-DCMAKE_INSTALL_PREFIX=$CPFE_PACKAGES/dealii_install ../dealii
*
which ran successfully. I have attached the file *detailed.log*. Then
installing via
*make -j8 install *
ran without issues. I have attached the output from the above command in the
file *make_output.txt*. Then running the tests as
*make -j4 test *
*
*
reports failure for all the tests. I have attached the entire output from the
above command in the file test_output.txt and an example error below :
2/11 Test #2: step.release .....................***Failed 0.69 sec
gmake[6]: *** read jobs pipe: Bad file descriptor. Stop.
gmake[6]: *** Waiting for unfinished jobs....
gmake[5]: *** [CMakeFiles/Makefile2:10861:
tests/quick_tests/CMakeFiles/step.release.run.dir/rule] Error 2
gmake[4]: *** [Makefile:3713: step.release.run] Error 2
Test step.release: BUILD
=============================== OUTPUT BEGIN ===============================
step.release: BUILD failed. Output:
[ 1%] Built target obj_boost_iostreams_release
step.release: ****** BUILD failed *******
=============================== OUTPUT END ===============================
Expected stage PASSED - aborting
CMake Error at
/global/project/projectdirs/m2360/packagesCPFE/dealii/cmake/scripts/run_test.cmake:140
(MESSAGE):
*** abort
I am unable to understand what the issue might. Any insight on this will be
appreciated. Thank you.
Best,
Aaditya
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