Hi Sjors,
This isn't a cluster, just multi-gpu workstation. I'm not sure I
understand your question, but the output I get from the command you
suggested is:
> > ldd `which relion_refine_mpi`
> linux-vdso.so.1 => (0x00007ffcffa19000)
> librelion_lib.so => /usr/bin/relion/lib/librelion_lib.so
> (0x00007f6e52ef9000)
> libmpi_cxx.so.1 => /usr/lib/libmpi_cxx.so.1 (0x00007f6e52cbc000)
> libmpi.so.12 => /usr/lib/libmpi.so.12 (0x00007f6e529e6000)
> libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0
> (0x00007f6e527c9000)
> libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
> (0x00007f6e52446000)
> libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1
> (0x00007f6e52230000)
> libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f6e51e66000)
> libfftw3.so.3 => /usr/lib/x86_64-linux-gnu/libfftw3.so.3
> (0x00007f6e51a67000)
> libfltk.so.1.3 => /usr/bin/relion/lib/libfltk.so.1.3
> (0x00007f6e5176d000)
> librelion_gpu_util.so => /usr/bin/relion/lib/librelion_gpu_util.so
> (0x00007f6e51315000)
> libcufft.so.8.0 => /usr/local/cuda-8.0/lib64/libcufft.so.8.0
> (0x00007f6e484c5000)
> libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f6e482c1000)
> librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f6e480b9000)
> libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f6e47daf000)
> libibverbs.so.1 => /usr/lib/libibverbs.so.1 (0x00007f6e47ba0000)
> libopen-rte.so.12 => /usr/lib/libopen-rte.so.12 (0x00007f6e47926000)
> libopen-pal.so.13 => /usr/lib/libopen-pal.so.13 (0x00007f6e47688000)
> /lib64/ld-linux-x86-64.so.2 (0x000056457a0f6000)
> libXfixes.so.3 => /usr/lib/x86_64-linux-gnu/libXfixes.so.3
> (0x00007f6e47482000)
> libXext.so.6 => /usr/lib/x86_64-linux-gnu/libXext.so.6
> (0x00007f6e4726f000)
> libX11.so.6 => /usr/lib/x86_64-linux-gnu/libX11.so.6
> (0x00007f6e46f35000)
> libhwloc.so.5 => /usr/lib/x86_64-linux-gnu/libhwloc.so.5
> (0x00007f6e46cfa000)
> libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1
> (0x00007f6e46af7000)
> libxcb.so.1 => /usr/lib/x86_64-linux-gnu/libxcb.so.1
> (0x00007f6e468d5000)
> libnuma.so.1 => /usr/lib/x86_64-linux-gnu/libnuma.so.1
> (0x00007f6e466c9000)
> libltdl.so.7 => /usr/lib/x86_64-linux-gnu/libltdl.so.7
> (0x00007f6e464bf000)
> libXau.so.6 => /usr/lib/x86_64-linux-gnu/libXau.so.6
> (0x00007f6e462bb000)
> libXdmcp.so.6 => /usr/lib/x86_64-linux-gnu/libXdmcp.so.6
> (0x00007f6e460b4000)
Regards,
-jh-
On 06/21/2017 01:08 PM, Sjors Scheres wrote:
> If you type
> ldd `which relion_refine_mpi`
> Does that also point to /usr/bin/mpirun?
> And is that also true for different cluster nodes? We install openMPI in a
> commonly accessible directory and compile relion with that. We then make
> sure that that mpirun is also used for running.
> best,Sjors
>
--
John M. Heumann
Department of Molecular, Cellular, and Developmental Biology
347 UCB, University of Colorado
Boulder, CO 80309-0347
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