Comments (4)
from eman2.
@sludtke42 : Thank you for your reply. I already tested yesterday to use our system OpenMPI (built with --enable-dlopen). EMAN 2.3 builds fine, but when running the test with "make test", I get an "undefined symbol error":
/cluster/apps/gcc-4.8.5/cmake-3.9.0-5yzdokxge3hk65gdzdfxw7wdzsv4pnfl/bin/ctest -V -C Release
UpdateCTestConfiguration from :/scratch/2409628.tmpdir/eman2-2.3/build/DartConfiguration.tcl
UpdateCTestConfiguration from :/scratch/2409628.tmpdir/eman2-2.3/build/DartConfiguration.tcl
Test project /scratch/2409628.tmpdir/eman2-2.3/build
Constructing a list of tests
Done constructing a list of tests
Updating test list for fixtures
Added 0 tests to meet fixture requirements
Checking test dependency graph...
Checking test dependency graph end
test 1
Start 1: imports
1: Test command: /cluster/apps/python/2.7.14/bin/python "/scratch/2409628.tmpdir/eman2-2.3/tests/test_imports.py"
1: Test timeout computed to be: 9.99988e+06
1: Traceback (most recent call last):
1: File "/scratch/2409628.tmpdir/eman2-2.3/tests/test_imports.py", line 3, in <module>
1: from libpyAligner2 import Aligners
1: ImportError: /cluster/apps/python/2.7.14/lib64/python2.7/site-packages/libEM2.so: undefined symbol: _ZN3MPI8Datatype4FreeEv
1/5 Test #1: imports ..........................***Failed 0.11 sec
test 2
Start 2: test-EMAN2DIR
2: Test command: /cluster/apps/python/2.7.14/bin/python "/scratch/2409628.tmpdir/eman2-2.3/tests/test_EMAN2DIR.py"
2: Test timeout computed to be: 9.99988e+06
2: Traceback (most recent call last):
2: File "/scratch/2409628.tmpdir/eman2-2.3/tests/test_EMAN2DIR.py", line 4, in <module>
2: import EMAN2
2: File "/cluster/apps/python/2.7.14/lib64/python2.7/site-packages/EMAN2.py", line 51, in <module>
2: from EMAN2_cppwrap import *
2: File "/cluster/apps/python/2.7.14/lib64/python2.7/site-packages/EMAN2_cppwrap.py", line 35, in <module>
2: from libpyAligner2 import *
2: ImportError: /cluster/apps/python/2.7.14/lib64/python2.7/site-packages/libEM2.so: undefined symbol: _ZN3MPI8Datatype4FreeEv
2/5 Test #2: test-EMAN2DIR ....................***Failed 0.38 sec
Checking the libEM2.so with readelf, showed that those symbols are not defined in the library:
[sfux@lo-a2-017 libEM]$ readelf -a libEM2.so | grep _ZN3MPI8Datatype4FreeEv
116: 0000000000000000 0 NOTYPE GLOBAL DEFAULT UND _ZN3MPI8Datatype4FreeEv
4457: 0000000000000000 0 NOTYPE GLOBAL DEFAULT UND _ZN3MPI8Datatype4FreeEv
[sfux@lo-a2-017 libEM]$
I am not really an OpenMPI expert, therefore I cannot judge, if this is caused by the dlopen issue.
Again, thank you for your help.
from eman2.
from eman2.
--disable-dlopen
shouldn't be needed with OpenMPI 3 and higher, open-mpi/ompi#3705 (comment).
from eman2.
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from eman2.