Import error- undefined symbol: __gmpq_add

[nambiarnik]

When I'm importing memsurfer, I get the following error:

ImportError: /home/nambinik/miniconda3/lib/python3.11/site-packages/memsurfer-1.1.0-py3.11-linux-x86_64.egg/memsurfer/_memsurfer_cmod.so: undefined symbol: __gmpq_add

I believe this might be due to the GMP library not being linked,

With inspiration from an earlier question #3 I added the libgmp libraries to setup.py and reinstalled memsurfer.

Specifically changed lines 228,234 and 235

include_dirs=[PATH_PM, numpy.get_include(),
PATHS['boost']['include'],
PATHS['eigen']['include'],
PATHS['cgal']['include'],
'/opt/local/include','/usr/include/x86_64-linux-gnu'
],
LIBS_EXT.append('gmp')
libraries=LIBS_EXT,
library_dirs=[PATHS['cgal']['lib'],'/usr/lib/x86_64-linux-gnu/']

Still get the same error though. How would one go about getting around this error?

Best
Nikhil

[andreashlarsen]

and the same issue as #24
I just tried to install again with a new student, starting the installation from scratch, but got the same error.

[lunamorrow]

Having the same error installing from scratch. I'm trying to set it up for someone else in my lab. She really wants to use and access Memsurfer for analysis so it would be great if someone can look into this error ASAP please!

[lunamorrow]

I followed these steps and then I was able to import MemSurfer. I hope this works for you too.

Hi @Rickk-B, thank you so much for replying! I've gone through the steps but unfortunately am still having issues with running python setup.py clean --all. It seems that gmp doesn't have a lib, as I am receiving:

library_dirs=[PATHS['cgal']['lib'], PATHS['gmp']['lib']],
                                        ~~~~~~~~~~~~^^^^^^^
KeyError: 'lib'

Do you have any tips? I suspect it may be an issue with my gmp install but I am not sure. I just used sudo apt-get install -y libgmp-dev, but I'll try a manual build from a tar and see if that helps.

[Rickk-B]

@lunamorrow, I've tried again and I think this is an easier fix than the previous one. This time I set up a new conda environment using an .yml file to ensure correct installations.

Creating the .yml file

name: simulation
channels:
conda-forge
defaults
dependencies:
gcc_linux-64=7.5.0
gxx_linux-64=7.5.0
python=3.7.12
cython=0.29.24
swig=4.0.2
cmake=3.20
gmp=6.2.1
mpfr=4.1.0
numpy
libxcrypt
scipy
mdanalysis

After creating the .yml file i followed these steps:

MemSurfer installation in clean conda environment

conda env create -f memsurfer.yml
conda activate simulation

Creating symlinks to the compilers

cd $CONDA_PREFIX/bin
ln -s x86_64-conda-linux-gnu-g++ g++
ln -s x86_64-conda-linux-gnu-gcc gcc
cd ../

Exporting paths

export CC="$CONDA_PREFIX/bin/gcc"
export CXX="$CONDA_PREFIX/bin/g++"
export CC_COMPILER=which gcc
export CXX_COMPILER=which g++
export LDCXXSHARED="$CXX -shared"
export PATH="$CONDA_PREFIX/bin/:$PATH"
export MEM_HOME="$CONDA_PREFIX/MemSurfer"
export PYTHONPATH="$CONDA_PREFIX/lib/python3.7/site-packages"
export LD_LIBRARY_PATH="$MEM_HOME/external/lib:$LD_LIBRARY_PATH"
export CGAL_ROOT="$MEM_HOME/external"
export EIGEN_ROOT="$MEM_HOME/external"
export BOOST_ROOT="$MEM_HOME/external"

Verification of correct paths and versions

which gcc
which g++
which python
echo $PATH
gcc --version
g++ --version

Downloading MemSurfer

git clone https://github.com/LLNL/MemSurfer.git
cd MemSurfer
git clone https://github.com/mmolero/pypoisson.git
cd pypoisson
git clone https://github.com/mmolero/PoissonRecon_v6_13.git
cd ../

Script change in setup.py

Add line 168: LIBS_EXT = ['CGAL','gmp']

Installing depencies and MemSurfer

cd $MEM_HOME
./install_deps.sh
python setup.py clean --all
python -m pip install .

Testing MemSurfer

import memsurfer