issue with importing memsurfer after installing with spack.

[Satya-Chaithanya-Duggisetty]

Python 3.7.7 (default, Jul 25 2020, 19:09:04) [GCC 7.5.0] on linux Type "help", "copyright", "credits" or "license" for more information.

import memsurfer Traceback (most recent call last): File "/home/satya/spack/opt/spack/linux-ubuntu18.04-haswell/gcc-7.5.0/memsurfer-1.0-5jeqsygjzxqh2bgh3sjq7wuljfgaiu5o/lib/python3.7/site-packages/memsurfer-1.0.0-py3.7-linux-x86_64.egg/memsurfer/pymemsurfer.py", line 14, in swig_import_helper return importlib.import_module(mname) File "/home/satya/spack/opt/spack/linux-ubuntu18.04-haswell/gcc-7.5.0/python-3.7.7-4juxjrlcplzzqfleofzbvfym2shujqqz/lib/python3.7/importlib/init.py", line 127, in import_module return _bootstrap._gcd_import(name[level:], package, level) File "", line 1006, in _gcd_import File "", line 983, in _find_and_load File "", line 965, in _find_and_load_unlocked ModuleNotFoundError: No module named 'memsurfer._pymemsurfer'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "", line 1, in File "/home/satya/spack/opt/spack/linux-ubuntu18.04-haswell/gcc-7.5.0/memsurfer-1.0-5jeqsygjzxqh2bgh3sjq7wuljfgaiu5o/lib/python3.7/site-packages/memsurfer-1.0.0-py3.7-linux-x86_64.egg/memsurfer/init.py", line 15, in from .membrane import Membrane File "/home/satya/spack/opt/spack/linux-ubuntu18.04-haswell/gcc-7.5.0/memsurfer-1.0-5jeqsygjzxqh2bgh3sjq7wuljfgaiu5o/lib/python3.7/site-packages/memsurfer-1.0.0-py3.7-linux-x86_64.egg/memsurfer/membrane.py", line 21, in from . import pymemsurfer File "/home/satya/spack/opt/spack/linux-ubuntu18.04-haswell/gcc-7.5.0/memsurfer-1.0-5jeqsygjzxqh2bgh3sjq7wuljfgaiu5o/lib/python3.7/site-packages/memsurfer-1.0.0-py3.7-linux-x86_64.egg/memsurfer/pymemsurfer.py", line 17, in _pymemsurfer = swig_import_helper() File "/home/satya/spack/opt/spack/linux-ubuntu18.04-haswell/gcc-7.5.0/memsurfer-1.0-5jeqsygjzxqh2bgh3sjq7wuljfgaiu5o/lib/python3.7/site-packages/memsurfer-1.0.0-py3.7-linux-x86_64.egg/memsurfer/pymemsurfer.py", line 16, in swig_import_helper return importlib.import_module('_pymemsurfer') File "/home/satya/spack/opt/spack/linux-ubuntu18.04-haswell/gcc-7.5.0/python-3.7.7-4juxjrlcplzzqfleofzbvfym2shujqqz/lib/python3.7/importlib/init.py", line 127, in import_module return _bootstrap._gcd_import(name[level:], package, level) ImportError: /home/satya/spack/opt/spack/linux-ubuntu18.04-haswell/gcc-7.5.0/memsurfer-1.0-5jeqsygjzxqh2bgh3sjq7wuljfgaiu5o/lib/python3.7/site-packages/memsurfer-1.0.0-py3.7-linux-x86_64.egg/_pymemsurfer.cpython-37m-x86_64-linux-gnu.so: undefined symbol: __gmpq_add

I have installed memsurfer using spack. GMP and MPFR were installed in the machine. when i was looking for solution, found this thread in the issues (https://github.com/LLNL/MemSurfer/issues/3) but i don't know how to implement this with spack.

Best regards Satya Chaithanya

[bhatiaharsh]

Hello Satya, I am not able to reproduce the issue. spack installation should automatically pick the gmp and mpfr used for compiling cgal and memsurfer. Can you send me the output of spack find -dvl memsurfer ?

By default, spack will install gmp and mpfr for you. But you say that they were installed on the machine, so did you make any modifications to point spack to those installations? Can you tell me what steps did you take exactly?

[Satya-Chaithanya-Duggisetty]

outpur of spack find -dvl memsurfer,

==> 1 installed package -- linux-ubuntu18.04-haswell / gcc@7.5.0 ------------------------ 5jeqsyg memsurfer@1.0+osmesa 24fxyg6 cgal@4.13~core~demos~imageio+shared build_type=Release 2qo6my3 boost@1.73.0+atomic+chrono~clanglibcpp~container~context~coroutine+date_time~debug+exception~fiber+filesystem+graph~icu+iostreams+locale+log+math~mpi+multithreaded~numpy~pic+program_options~python+random+regex+serialization+shared+signals~singlethreaded+system~taggedlayout+test+thread+timer~versionedlayout+wave cxxstd=98 patches=246508e052c44b6f4e8c2542a71c06cacaa72cd1447ab8d2a542b987bc35ace9,4dd507e1f5a29e3b87b15321a4d8c74afdc8331433edabf7aeab89b3c405d556 visibility=hidden odnxdc3 bzip2@1.0.8+shared zkl5ufy zlib@1.2.11+optimize+pic+shared 66a4wp2 gmp@6.1.2 i5c35gu mpfr@4.0.2 patches=3f80b836948aa96f8d1cb9cc7f3f55973f19285482a96f9a4e1623d460bcccf0 h325s5c eigen@3.3.7 build_type=RelWithDebInfo zjpbg5v hdf5@1.10.6~cxx~debug~fortran+hl~mpi+pic+shared~szip~threadsafe api=none 7ibpulp py-numpy@1.19.1+blas+lapack qzy5vz5 openblas@0.3.10~consistent_fpcsr~ilp64+pic+shared threads=none 4juxjrl python@3.7.7+bz2+ctypes+dbm~debug+libxml2+lzma~nis~optimizations+pic+pyexpat+pythoncmd+readline+shared+sqlite3+ssl~tix~tkinter~ucs4~uuid+zlib patches=0d98e93189bc278fbc37a50ed7f183bd8aaf249a8e1670a465f0db6bb4f8cf87 3sylp4j expat@2.2.9+libbsd fzzuj57 libbsd@0.10.0 7xayw7d gdbm@1.18.1 m223ipe readline@8.0 yillvg4 ncurses@6.2~symlinks+termlib 3nufwnh gettext@0.20.2+bzip2+curses+git~libunistring+libxml2+tar+xz dtlc732 libiconv@1.16 5ocv57r libxml2@2.9.10~python 3q6gncb xz@5.2.5 ubjpbg3 tar@1.32 pmtijtm libffi@3.3 patches=26f26c6f29a7ce9bf370ad3ab2610f99365b4bdd7b82e7c31df41a3370d685c0 7pplabt openssl@1.1.1g+systemcerts yalztzz sqlite@3.31.1+column_metadata+fts~functions~rtree 2u3pqv3 vtk@8.1.2~ffmpeg~mpi+opengl2+osmesa+python~qt~xdmf build_type=RelWithDebInfo jsmrog5 freetype@2.10.1 6jvpgru libpng@1.6.37 2vn7r7c glew@2.0.0 qhkn2hm libice@1.0.9 miiqmwu libsm@1.2.2 zgpiqr5 libuuid@1.0.3 vtay7am mesa@18.3.6+glx+llvm+opengl~opengles+osmesa patches=55a5611ca9fcbe8324c4d68a07b338134954ff12c5b122dc78ff376f012a1414 swr=none mo4rpsp libx11@1.6.7 35iul4o kbproto@1.0.7 2juhxb4 libxcb@1.13 ahhyn3z libpthread-stubs@0.4 t2lao5s libxau@1.0.8 hl5jkoc xproto@7.0.31 qt76not libxdmcp@1.1.2 rxfy3dr xextproto@7.3.0 55vjugr libxext@1.3.3 6gf2acu llvm@10.0.0~all_targets+clang~code_signing+compiler-rt~cuda+gold+internal_unwind+libcxx+lld+lldb~mlir~omp_debug~omp_tsan+polly~python~shared_libs~split_dwarf build_type=Release cuda_arch=none patches=332fe65f78b2b4a242045ec2394eee8db631fbcbe27b0016d5e5c859e34f47af h2xcnnn binutils@2.34+gold~headers~interwork~ld~libiberty~lto+nls~plugins x7yadtu hwloc@2.2.0~cairo~cuda~gl~libudev+libxml2~netloc~nvml+pci+shared zlvpt6m libpciaccess@0.13.5 eas54lx libedit@3.1-20191231 apld5vq swig@3.0.12 hjqurur pcre@8.44~jit+multibyte+utf n7xqhzb z3@4.8.7+python zd3a3pc py-setuptools@46.1.3 t5ylwte jsoncpp@1.9.2 build_type=RelWithDebInfo cxxstd=default 6pm27f7 libjpeg-turbo@2.0.4 npoknir libtiff@4.0.10 qjdxaef lz4@1.9.2 zb3a3wj netcdf-c@4.7.3~dap~hdf4~jna~mpi~parallel-netcdf+pic+shared dzhqsc3 netcdf-cxx@4.2+netcdf4

I haven't changed any modifications to point spack to gmp or mpfr installations, I don't remember the name of the package, one of the package constantly getting terminated without getting installed using spack. when i kept the error in online i got comand line solution to install gmp and mpfr. Then the package got installed.