[gmx-users] Can't run v. 4.6.6 on worker nodes if they are compiled with SIMD

[Mark Abraham]

On Sat, Jul 26, 2014 at 7:35 PM, Seyyed Mohtadin Hashemi <haadah at gmail.com>
wrote:

> On Jul 26, 2014 4:52 AM, "Mark Abraham" <mark.j.abraham at gmail.com> wrote:
> >
> > Hi,
> >
> > That is indeed very weird - particularly if compiling on the compute
> nodes
> > with GPU support enabled gives the same result. Both host and compute
> nodes
> > support rdtscp, so that known suspect is OK. I can only guess that
> there's
> > something in the CUDA installation process that targets the CPU on the
> > install host. Configuring with -DCMAKE_BUILD_TYPE=Debug and getting a
> stack
> > trace from the crash might help work out where the problem arises.
>
> Will get back with the stack trace a bit later; is "gdb bt full" ok?


Probably.

Mark


> Or do
> you want "thread info" as well?
>
> Doing a
> > CUDA install on a compute node and compiling against that might help.
>
> You mean install CUDA SDK on the worker nodes? If so, this is already done
> and gives same result. I will ask the admin about the configuration of CUDA
> on the worker nodes.
> >
> > Mark
> >
> >
> >
> > On Fri, Jul 25, 2014 at 10:00 PM, Seyyed Mohtadin Hashemi <
> haadah at gmail.com>
> > wrote:
> >
> > > Hi everyone,
> > >
> > > I'm having a very weird problem with GROMACS 4.6.6:
> > >
> > > I am currently testing out GPU capabilities and was trying to compile
> > > GROMACS with CUDA (v6.0). I can not make this work if I compile GROMACS
> > > with SIMD, no matter what kernel I choose - I have tried everything
> from
> > > SSE2 to AVX_256.
> > >
> > > The log-in node, where I compile, has AMD Interlagos CPUs (worker nodes
> use
> > > Xeon E5-2630 and are equipped with Tesla K20), but I do not think this
> is
> > > the problem - I have compiled GROMACS, using the log-in node, without
> CUDA
> > > but with AVX_256 SIMD and everything works. As soon as CUDA is added to
> the
> > > mix, I get "Illegal Instruction" every time I try to run on the worker
> > > nodes.
> > >
> > > Compiling on worker nodes gives the same result. However, as soon as I
> set
> > > SIMD=None everything works and I am able to run simulation using GPUs,
> this
> > > is regardless of if I use log-in node or worker node to compile.
> > >
> > >
> > > The cmake string used to configure is:
> > > ccmake .. -DCMAKE_INSTALL_PREFIX=/work/gromacs4gpu -DGMX_DOUBLE=OFF
> > > -DGMX_DEFAULT_SUFFIX=OFF -DGMX_BINARY_SUFFIX=_4gpu
> -DGMX_LIBS_SUFFIX=_4gpu
> > > -DGMX_GPU=ON -DBUILD_SHARED_LIBS=OFF -DGMX_PREFER_STATIC_LIBS=ON
> > > -GMX_MPI=OFF -DGMX_CPU_ACCELERATION=AVX_256
> > >
> > > CUDA v6.0 and FFTW v3.3.4 (single precision) libs are set globally and
> > > correctly identified by GROMACS. To remove OpenMPI as a problem I am
> > > compiling without it (compiling with OpenMPI produced the same behavior
> as
> > > without), once I have found the error I will compile with OpenMPI
> v1.6.5.
> > >
> > > I get these warnings during the configuration, nothing important:
> > >
> > >  A BLAS library was not found by CMake in the paths available to it.
> > > Falling back on the GROMACS internal version of the BLAS library
> instead.
> > > This is fine for normal usage.
> > >
> > >  A LAPACK library was not found by CMake in the paths available to it.
> > > Falling back on the GROMACS internal version of the LAPACK library
> instead.
> > > This is fine for normal usage.
> > >
> > > I am currently trying to compile and test GROMACS 5.0 to see if it also
> > > exhibits the same behavior.
> > >
> > > I hope that someone can point me in the direction of a possible
> solution,
> > > if not then I will file a bug report.
> > >
> > > Regards,
> > > Mohtadin
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>