undefined symbol with openmm anaconda

[hainm]

Hi,
I am not sure if my question here is in right place or not, but I install via 'omnia' channel, so ...

install

conda install -c omnia openmm --force

run

python -c 'from simtk import openmm

get error

ImportError: /home/haichit/anaconda3/lib/python3.4/site-packages/simtk/openmm/_openmm.cpython-34m.so: undefined symbol: _ZZN4swig11traits_infoISt3mapIiiSt4lessIiESaISt4pairIKiiEEEE9type_infoEvE4info

any idea why this happens? thanks

[rmcgibbo]

my guess is that you have an older version of openmm in your LD_LIBRARY_PATH (or DYLD_LIBRARY_PATH).

[hainm]

@rmcgibbo any idea how to check that?

I tried to locate and delete all simtk folder and reinstall, still got same error.

locate _openmm.cpython-34m.so
`/u1/haichit/anaconda3/lib/python3.4/site-packages/simtk/openmm/_openmm.cpython-34m.so
/u1/haichit/anaconda3/pkgs/openmm-6.3-py34_0/lib/python3.4/site-packages/simtk/openmm/_openmm.cpython-34m.so

[jchodera]

Have you tried this in a clean miniconda install? I find I have to flush mine out every once in a while.

Before you try that, you should try uninstalling the openmm and openmm-dev packages and clearing out your caches:

conda remove --yes openmm openmm-dev
conda clean -ptls --yes
conda install --yes openmm-dev

[hainm]

Have you tried this in a clean miniconda install? I find I have to flush mine out every once in a while.

openmm works fine in one of my machine.

Before you try that, you should try uninstalling the openmm and openmm-dev packages and clearing out your caches:

I copied and paste your commands but got same error. Probably I messed up somewhere, may be because I tried to install gcc and libgcc by conda.

[hainm]

conda clean -ptls --yes

this one seems dangerous. It destroyed my ipython.

[rmcgibbo]

$ echo $LD_LIBRARY_PATH

[hainm]

$ echo $LD_LIBRARY_PATH

sorry, I mean, what should I look for in $LD_LIBRARY_PATH?

[jchodera]

Conda clean only clears caches. There is no way it should have an impact on installed packages.

That said, conda still seems buggy. There can be times where valid conda commands leave the packaged manager in an undefined state.

[rmcgibbo]

The cause of the undefined symbol import error you posted is that the linker is loading up a different version of libOpenMM.so than the one that the python wrappers were build with. This can be caused, for example, if you installed openmm 6.2 from source, and then conda-install openmm 6.3. Or something similar. So you should be looking for another version of openmm that's ahead in the linker path.

[hainm]

I tried to locate

$ locate libOpenMM.so
/u1/haichit/anaconda3/lib/libOpenMM.so

Not sure where else.

Here is all the "OpenMM" files in my path

In [2]: pt.tools.find_lib('OpenMM')
Out[2]:
['/home/haichit/anaconda3//lib/libOpenMMAmoeba.so',
 '/home/haichit/anaconda3//lib/libOpenMMRPMD.so',
 '/home/haichit/anaconda3//lib/libOpenMMDrude.so',
 '/home/haichit/anaconda3//lib/libOpenMM.so']

[rmcgibbo]

You might have more luck with ldd or strace.

[hainm]

no luck. I tried to create new envs, got the same error. this is how ldd show

$ ldd /home/haichit/anaconda3/envs/openmm/lib/python3.4/site-
packages/simtk/openmm/_openmm.cpython-34m.so
        linux-vdso.so.1 =>  (0x00007fffe47f5000)
        libOpenMM.so => /home/haichit/anaconda3/envs/openmm/lib/python3.4/site-
packages/simtk/openmm/../../../../libOpenMM.so (0x00002ab758b45000)
        libOpenMMAmoeba.so => /home/haichit/anaconda3/envs/openmm/lib/python3.4/site-
packages/simtk/openmm/../../../../libOpenMMAmoeba.so (0x00002ab75901a000)
        libOpenMMRPMD.so => /home/haichit/anaconda3/envs/openmm/lib/python3.4/site-
packages/simtk/openmm/../../../../libOpenMMRPMD.so (0x00002ab75928c000)
        libOpenMMDrude.so => /home/haichit/anaconda3/envs/openmm/lib/python3.4/site-
packages/simtk/openmm/../../../../libOpenMMDrude.so (0x00002ab75949b000)
        libpython3.4m.so.1.0 => /home/haichit/anaconda3/envs/openmm/lib/python3.4/site-
packages/simtk/openmm/../../../../libpython3.4m.so.1.0 (0x00002ab7596ad000)
        libstdc++.so.6 => /home/haichit/anaconda3//lib/libstdc++.so.6 (0x00002ab759b58000)
        libm.so.6 => /lib64/libm.so.6 (0x00002ab759e84000)
        libgcc_s.so.1 => /home/haichit/anaconda3//lib/libgcc_s.so.1 (0x00002ab75a107000)
        libpthread.so.0 => /lib64/libpthread.so.0 (0x00002ab75a31d000)
        libc.so.6 => /lib64/libc.so.6 (0x00002ab75a539000)
        librt.so.1 => /lib64/librt.so.1 (0x00002ab75a891000)
        libdl.so.2 => /lib64/libdl.so.2 (0x00002ab75aa9a000)
        libutil.so.1 => /lib64/libutil.so.1 (0x00002ab75ac9f000)
        /lib64/ld-linux-x86-64.so.2 (0x00000036a1200000)