Hi everyone, I installed firedrake onto our local KNL box which runs on CentOS 7.4, so I managed to install all the necessary requirements using --no-package-manager. The installation returns no error but I am seeing this error: (firedrake) [root@caamhpc ~]# python -c "from firedrake import *" Traceback (most recent call last): File "<string>", line 1, in <module> File "/root/Software/firedrake/src/firedrake/firedrake/__init__.py", line 29, in <module> from pyop2 import op2 # noqa File "/root/Software/firedrake/src/PyOP2/pyop2/__init__.py", line 4, in <module> from pyop2.op2 import * # noqa File "/root/Software/firedrake/src/PyOP2/pyop2/op2.py", line 42, in <module> from pyop2.base import i # noqa: F401 File "/root/Software/firedrake/src/PyOP2/pyop2/base.py", line 57, in <module> from pyop2.sparsity import build_sparsity ImportError: /root/Software/firedrake/src/PyOP2/pyop2/ sparsity.cpython-36m-x86_64-linux-gnu.so: undefined symbol: _intel_fast_memset I have never seen this before. Here's some information that may be helpful: (firedrake) [root@caamhpc ~]# ldd /root/Software/firedrake/src/PyOP2/pyop2/ sparsity.cpython-36m-x86_64-linux-gnu.so linux-vdso.so.1 => (0x00007fffc8f54000) libpetsc.so.3.07 => /root/Software/firedrake/lib/python3.6/site-packages/petsc/lib/libpetsc.so.3.07 (0x00007fbf5e1f0000) libpython3.6m.so.1.0 => /usr/local/lib/libpython3.6m.so.1.0 (0x00007fbf5dcb9000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fbf5da86000) libc.so.6 => /lib64/libc.so.6 (0x00007fbf5d6c2000) liblapack.so.3 => /lib64/liblapack.so.3 (0x00007fbf5cf64000) libblas.so.3 => /lib64/libblas.so.3 (0x00007fbf5cd0b000) libparmetis.so => /root/Software/firedrake/lib/python3.6/site-packages/petsc/lib/libparmetis.so (0x00007fbf5cacf000) libmetis.so => /root/Software/firedrake/lib/python3.6/site-packages/petsc/lib/libmetis.so (0x00007fbf5c858000) libhdf5hl_fortran.so.10 => /root/Software/firedrake/lib/python3.6/site-packages/petsc/lib/libhdf5hl_fortran.so.10 (0x00007fbf5c645000) libhdf5_fortran.so.10 => /root/Software/firedrake/lib/python3.6/site-packages/petsc/lib/libhdf5_fortran.so.10 (0x00007fbf5c409000) libhdf5_hl.so.10 => /root/Software/firedrake/lib/python3.6/site-packages/petsc/lib/libhdf5_hl.so.10 (0x00007fbf5c1e7000) libhdf5.so.10 => /root/Software/firedrake/lib/python3.6/site-packages/petsc/lib/libhdf5.so.10 (0x00007fbf5bd08000) libm.so.6 => /lib64/libm.so.6 (0x00007fbf5ba06000) libgfortran.so.3 => /lib64/libgfortran.so.3 (0x00007fbf5b6e3000) libquadmath.so.0 => /lib64/libquadmath.so.0 (0x00007fbf5b4a7000) libmpicxx.so.12 => /opt/intel/compilers_and_libraries_2016.3.210/linux/mpi/intel64/lib/libmpicxx.so.12 (0x00007fbf5b287000) libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007fbf5af7e000) libdl.so.2 => /lib64/libdl.so.2 (0x00007fbf5ad7a000) libmpifort.so.12 => /opt/intel/compilers_and_libraries_2016.3.210/linux/mpi/intel64/lib/libmpifort.so.12 (0x00007fbf5a9dc000) libmpi.so.12 => /opt/intel/compilers_and_libraries_2016.3.210/linux/mpi/intel64/lib/libmpi.so.12 (0x00007fbf5a20c000) librt.so.1 => /lib64/librt.so.1 (0x00007fbf5a004000) libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007fbf59dee000) libutil.so.1 => /lib64/libutil.so.1 (0x00007fbf59bea000) /lib64/ld-linux-x86-64.so.2 (0x00007fbf5f8b9000) (firedrake) [root@caamhpc ~]# which mpicc /opt/intel/compilers_and_libraries_2016.3.210/linux/mpi/intel64/bin/mpicc (firedrake) [root@caamhpc ~]# mpicc --version gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-16) Copyright (C) 2015 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. This system wants to use intel compilers but I told it to use GNU compilers. I suspect this error has something to do with intel. I can try and provide more information as necessary. Thanks, Justin
Clearly, the problem is that the compiler you used linked to some Intel library, but the dynamic linker resolves to another shared object, so the referred symbol _intel_fast_memset is missing. Can you see any libraries in /opt/intel/compilers_and_libraries_2016.3.210/linux/mpi/intel64/lib/ that are resolved to some other path? For example, is there a librt.so.1 in that directory? ________________________________ From: firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of Justin Chang <jychang48@gmail.com> Sent: 18 October 2017 22:25:25 To: firedrake Subject: [firedrake] Problem with PyOP2 on KNL machine Hi everyone, I installed firedrake onto our local KNL box which runs on CentOS 7.4, so I managed to install all the necessary requirements using --no-package-manager. The installation returns no error but I am seeing this error: (firedrake) [root@caamhpc ~]# python -c "from firedrake import *" Traceback (most recent call last): File "<string>", line 1, in <module> File "/root/Software/firedrake/src/firedrake/firedrake/__init__.py", line 29, in <module> from pyop2 import op2 # noqa File "/root/Software/firedrake/src/PyOP2/pyop2/__init__.py", line 4, in <module> from pyop2.op2 import * # noqa File "/root/Software/firedrake/src/PyOP2/pyop2/op2.py", line 42, in <module> from pyop2.base import i # noqa: F401 File "/root/Software/firedrake/src/PyOP2/pyop2/base.py", line 57, in <module> from pyop2.sparsity import build_sparsity ImportError: /root/Software/firedrake/src/PyOP2/pyop2/sparsity.cpython-36m-x86_64-linux-gnu.so<http://sparsity.cpython-36m-x86_64-linux-gnu.so>: undefined symbol: _intel_fast_memset I have never seen this before. Here's some information that may be helpful: (firedrake) [root@caamhpc ~]# ldd /root/Software/firedrake/src/PyOP2/pyop2/sparsity.cpython-36m-x86_64-linux-gnu.so<http://sparsity.cpython-36m-x86_64-linux-gnu.so> linux-vdso.so.1 => (0x00007fffc8f54000) libpetsc.so.3.07 => /root/Software/firedrake/lib/python3.6/site-packages/petsc/lib/libpetsc.so.3.07 (0x00007fbf5e1f0000) libpython3.6m.so.1.0 => /usr/local/lib/libpython3.6m.so.1.0 (0x00007fbf5dcb9000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fbf5da86000) libc.so.6 => /lib64/libc.so.6 (0x00007fbf5d6c2000) liblapack.so.3 => /lib64/liblapack.so.3 (0x00007fbf5cf64000) libblas.so.3 => /lib64/libblas.so.3 (0x00007fbf5cd0b000) libparmetis.so => /root/Software/firedrake/lib/python3.6/site-packages/petsc/lib/libparmetis.so (0x00007fbf5cacf000) libmetis.so => /root/Software/firedrake/lib/python3.6/site-packages/petsc/lib/libmetis.so (0x00007fbf5c858000) libhdf5hl_fortran.so.10 => /root/Software/firedrake/lib/python3.6/site-packages/petsc/lib/libhdf5hl_fortran.so.10 (0x00007fbf5c645000) libhdf5_fortran.so.10 => /root/Software/firedrake/lib/python3.6/site-packages/petsc/lib/libhdf5_fortran.so.10 (0x00007fbf5c409000) libhdf5_hl.so.10 => /root/Software/firedrake/lib/python3.6/site-packages/petsc/lib/libhdf5_hl.so.10 (0x00007fbf5c1e7000) libhdf5.so.10 => /root/Software/firedrake/lib/python3.6/site-packages/petsc/lib/libhdf5.so.10 (0x00007fbf5bd08000) libm.so.6 => /lib64/libm.so.6 (0x00007fbf5ba06000) libgfortran.so.3 => /lib64/libgfortran.so.3 (0x00007fbf5b6e3000) libquadmath.so.0 => /lib64/libquadmath.so.0 (0x00007fbf5b4a7000) libmpicxx.so.12 => /opt/intel/compilers_and_libraries_2016.3.210/linux/mpi/intel64/lib/libmpicxx.so.12 (0x00007fbf5b287000) libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007fbf5af7e000) libdl.so.2 => /lib64/libdl.so.2 (0x00007fbf5ad7a000) libmpifort.so.12 => /opt/intel/compilers_and_libraries_2016.3.210/linux/mpi/intel64/lib/libmpifort.so.12 (0x00007fbf5a9dc000) libmpi.so.12 => /opt/intel/compilers_and_libraries_2016.3.210/linux/mpi/intel64/lib/libmpi.so.12 (0x00007fbf5a20c000) librt.so.1 => /lib64/librt.so.1 (0x00007fbf5a004000) libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007fbf59dee000) libutil.so.1 => /lib64/libutil.so.1 (0x00007fbf59bea000) /lib64/ld-linux-x86-64.so.2 (0x00007fbf5f8b9000) (firedrake) [root@caamhpc ~]# which mpicc /opt/intel/compilers_and_libraries_2016.3.210/linux/mpi/intel64/bin/mpicc (firedrake) [root@caamhpc ~]# mpicc --version gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-16) Copyright (C) 2015 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. This system wants to use intel compilers but I told it to use GNU compilers. I suspect this error has something to do with intel. I can try and provide more information as necessary. Thanks, Justin
participants (2)
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Homolya, Miklós
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Justin Chang