[gmx-users] gromacs 2018 for GPU install on cluster with truly static libraries?

Shayna Hilburg shilburg at mit.edu
Mon Jul 23 02:51:01 CEST 2018


Thank you!
I see these:

linux-vdso.so.1 =>  (0x00007ffc4f0df000)

libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0
(0x00007f10b6b51000)

libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f10b694d000)

librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f10b6745000)

libcufft.so.8.0 => /mnt/shared/cuda8/lib64/libcufft.so.8.0
(0x00007f10ad8f6000)

libmkl_intel_lp64.so => /home/shayna/miniconda3/lib/libmkl_intel_lp64.so
(0x00007f10acde3000)

libmkl_intel_thread.so =>
/home/shayna/miniconda3/lib/libmkl_intel_thread.so (0x00007f10aaa15000)

libmkl_core.so => /home/shayna/miniconda3/lib/libmkl_core.so
(0x00007f10a69e3000)

libiomp5.so => /home/shayna/miniconda3/lib/libiomp5.so (0x00007f10a6608000)

libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f10a62ff000)

libstdc++.so.6 => /home/shayna/miniconda3/lib/libstdc++.so.6
(0x00007f10a5fc5000)

libgcc_s.so.1 => /home/shayna/miniconda3/lib/libgcc_s.so.1
(0x00007f10a5db3000)

libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f10a59e9000)

/lib64/ld-linux-x86-64.so.2 (0x00007f10b6d6e000)

Is there a simple way to get all of these or a suggestion for a better way
to run gromacs on our computing cluster?

Thanks,
Shayna



On Sun, Jul 22, 2018 at 8:11 PM Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> CMake will link to whatever it is allowed to find. What does ldd on the
> executable report as the libraries being dynamically linked? Those are the
> ones that cmake found for which there were apparently no static
> equivalents.
>
> Mark
>
> On Sun, Jul 22, 2018, 18:16 Shayna Hilburg <shilburg at mit.edu> wrote:
>
> > Hi all,
> >
> > I'm trying to install GROMACS 2018 for use on GPUs. We typically keep the
> > software on the master node and just call it through a mounted drive on
> the
> > compute nodes. However, despite using static library tags, it appears
> there
> > are still dependencies. It works fine on our master node but not on the
> > compute nodes yet.
> > Does anyone have a method for installing and reliably running GROMACS in
> > this way (with all libraries in a prescribed location)? Any help would be
> > appreciated please! At least a list of which libraries we need to
> manually
> > install
> >
> > Some information:
> > -We tried these 2 different install methods in our efforts:
> > cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
> -DGMX_GPU=on
> > -DCMAKE_INSTALL_PREFIX=/mnt/shared/gromacs2018 -DBUILD_SHARED_LIBS=OFF
> > -DGMX_FFT_LIBRARY=fftw3 -DCUDA_TOOLKIT_ROOT_DIR=/mnt/shared/cuda8
> > -DGMX_PREFER_STATIC_LIBS=ON
> >
> > *cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
> -DGMX_GPU=on
> > -DCMAKE_INSTALL_PREFIX=/mnt/shared/gromacs2018 -DGMX_BUILD_SHARED_EXE=OFF
> > -DGMX_FFT_LIBRARY=fftw3 -DCUDA_TOOLKIT_ROOT_DIR=/mnt/shared/cuda8*
> >
> > Thank you!
> > Shayna
> >
> >
> > --
> >
> >
> > Shayna Hilburg
> > Doctoral Candidate
> > Massachusetts Institute of Technology
> > Department of Materials Science and Engineering
> > Program in Polymers and Soft Matter
> > Alexander-Katz <http://soft-materials.scripts.mit.edu/www/> Group
> > --
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