[gmx-users] Compilation issues with Gromacs 5.1.1 and SGI MPT

Thu Jan 7 19:27:25 CET 2016

Great. Thanks.

Hubert

2016-01-07 18:33 GMT+01:00 Mark Abraham <mark.j.abraham at gmail.com>:

> Hi,
>
> Thanks, I have now proposed that fix at https://gerrit.gromacs.org/5535.
> If
> accepted, it'll be in GROMACS 5.1.2
>
> Mark
>
> On Thu, Jan 7, 2016 at 6:05 PM Hubert Santuz <hubert.santuz at gmail.com>
> wrote:
>
> > Finally, I found a solution by digging on MPT C++ bindings.
> > In fact, at the end of the MPT mpi.h file, we have:
> >
> > if !defined(MPI_NO_CPPBIND)
> > #include "mpi++.h"
> > #endif
> >
> > So MPT expose the C++ bindings by default.
> > To prevent that, I add the macro to src/gromacs/utility/gmxmpi.h :
> >
> > /* MPI C++ binding is deprecated and can cause name conflicts (e.g.
> > stdio/mpi seek) */
> > #define MPICH_SKIP_MPICXX 1
> > #define OMPI_SKIP_MPICXX 1
> > #define MPI_NO_CPPBIND 1
> > #include <mpi.h>
> >
> > Since there is already macros for Mpich and OpenMPI, will it be worth it
> to
> > add the one from MPT and file a bug report?
> >
> > Cheers,
> > Hubert
> >
> >
> >
> > 2016-01-07 16:07 GMT+01:00 Mark Abraham <mark.j.abraham at gmail.com>:
> >
> > > Hi,
> > >
> > > No, I don't have access to the MPT documentation, so you should start
> > > there. I would be pretty sure it wouldn't be faster, either ;-)
> > >
> > > Mark
> > >
> > > On Thu, 7 Jan 2016 13:25 Hubert Santuz <hubert.santuz at gmail.com>
> wrote:
> > >
> > > > Hi,
> > > >
> > > > 2016-01-07 11:48 GMT+01:00 Mark Abraham <mark.j.abraham at gmail.com>:
> > > >
> > > > > Hi,
> > > > >
> > > > > On Thu, Jan 7, 2016 at 11:30 AM Hubert Santuz <
> > hubert.santuz at gmail.com
> > > >
> > > > > wrote:
> > > > >
> > > > > > Hi Mark,
> > > > > >
> > > > > > You were right, MPT defines a constant UNDEFINED in their mpi++.h
> > Why
> > > > it
> > > > > > should not do?
> > > > > >
> > > > >
> > > > > Because if everybody wrote libraries like that, then nobody could
> use
> > > any
> > > > > generic-sounding name for a symbol in their code, for fear of a
> clash
> > > > like
> > > > > the one you experienced. Symbols that libraries intend to export
> need
> > > to
> > > > > have names that are unlikely to clash with other libraries, or with
> > > user
> > > > > code. And libraries shouldn't define symbols they don't intend to
> > > define
> > > > > (which is probably what is happening here). If you let people park
> > > their
> > > > > cars wherever they want, you get chaos, right? :-)
> > > > >
> > > > >
> > > > Yeah, it makes sense...
> > > >
> > > >
> > > >
> > > > > When renaming gromacs one with GMX_UNDEFINED, the compilation
> suceed
> > > but
> > > > > > now I have linking issues (which I didn't have with OpenMPI):
> > > > > >
> > > > >
> > > > > Turn off the C++ bindings for MPI in MPT. Nobody uses them,
> > > particularly
> > > > > not GROMACS, and clearly they are tricky to link correctly.
> > > > >
> > > >
> > > > Do you have an idea on how to do that ? MPT is shipped as RPM
> package.
> > > > I tried to remove any variable linked to MPI_CXX in the gromacs cmake
> > > > without success.
> > > >
> > > >
> > > > >
> > > > >
> > > > > > [ 98%] Built target libgromacs
> > > > > > [ 98%] Built target mdrun_objlib
> > > > > > [100%] Linking CXX executable ../../bin/mdrun_mpi
> > > > > > CMakeFiles/mdrun_objlib.dir/mdrun/md.cpp.o: dans la fonction «
> > > > > > PMPI::Op::Init(void (*)(void const*, void*, int, PMPI::Datatype
> > > > const&),
> > > > > > bool) »:
> > > > > >
> > > > > >
> > > > >
> > > >
> > >
> >
> md.cpp:(.text._ZN4PMPI2Op4InitEPFvPKvPviRKNS_8DatatypeEEb[_ZN4PMPI2Op4InitEPFvPKvPviRKNS_8DatatypeEEb]+0x16):
> > > > > > undefined reference to « op_intercept(void*, void*, int*,
> unsigned
> > > > int*)
> > > > > »
> > > > > > CMakeFiles/mdrun_objlib.dir/mdrun/md.cpp.o: dans la fonction «
> > > > > > PMPI::Comm::Free() »:
> > > > > > md.cpp:(.text._ZN4PMPI4Comm4FreeEv[_ZN4PMPI4Comm4FreeEv]+0x13):
> > > > undefined
> > > > > > reference to « PMPI::Comm::mpi_comm_map »
> > > > > > md.cpp:(.text._ZN4PMPI4Comm4FreeEv[_ZN4PMPI4Comm4FreeEv]+0x1a):
> > > > undefined
> > > > > > reference to « PMPI::Comm::mpi_comm_map »
> > > > > > md.cpp:(.text._ZN4PMPI4Comm4FreeEv[_ZN4PMPI4Comm4FreeEv]+0x2f):
> > > > undefined
> > > > > > reference to « PMPI::Comm::mpi_comm_map »
> > > > > > CMakeFiles/mdrun_objlib.dir/mdrun/md.cpp.o: dans la fonction «
> > > > > > PMPI::Comm::Sendrecv_replace(void*, int, PMPI::Datatype const&,
> > int,
> > > > int,
> > > > > > int, int) const »:
> > > > > >
> > > > > >
> > > > >
> > > >
> > >
> >
> md.cpp:(.text._ZNK4PMPI4Comm16Sendrecv_replaceEPviRKNS_8DatatypeEiiii[_ZNK4PMPI4Comm16Sendrecv_replaceEPviRKNS_8DatatypeEiiii]+0xd):
> > > > > > undefined reference to « PMPI::Comm::ignored_status »
> > > > > > CMakeFiles/mdrun_objlib.dir/mdrun/md.cpp.o: dans la fonction «
> > > > > > PMPI::Comm::Sendrecv(void const*, int, PMPI::Datatype const&,
> int,
> > > int,
> > > > > > void*, int, PMPI::Datatype const&, int, int) const »:
> > > > > >
> > > > > >
> > > > >
> > > >
> > >
> >
> md.cpp:(.text._ZNK4PMPI4Comm8SendrecvEPKviRKNS_8DatatypeEiiPviS5_ii[_ZNK4PMPI4Comm8SendrecvEPKviRKNS_8DatatypeEiiPviS5_ii]+0xd):
> > > > > > undefined reference to « PMPI::Comm::ignored_status »
> > > > > > CMakeFiles/mdrun_objlib.dir/mdrun/md.cpp.o: dans la fonction «
> > > > > > PMPI::Comm::Probe(int, int) const »:
> > > > > >
> > md.cpp:(.text._ZNK4PMPI4Comm5ProbeEii[_ZNK4PMPI4Comm5ProbeEii]+0x8):
> > > > > > undefined reference to « PMPI::Comm::ignored_status »
> > > > > > CMakeFiles/mdrun_objlib.dir/mdrun/md.cpp.o: dans la fonction «
> > > > > > PMPI::Comm::Iprobe(int, int) const »:
> > > > > >
> > > md.cpp:(.text._ZNK4PMPI4Comm6IprobeEii[_ZNK4PMPI4Comm6IprobeEii]+0x12):
> > > > > > undefined reference to « PMPI::C
> > > > > > (...)
> > > > > >
> > > > > >
> > > > >
> > > >
> > >
> >
> md.cpp:(.text._ZNK4PMPI9Intracomm11Create_cartEiPKiPKbb[_ZNK4PMPI9Intracomm11Create_cartEiPKiPKbb]+0x190):
> > > > > > undefined reference to « MPI::Is_initialized() »
> > > > > > CMakeFiles/mdrun_objlib.dir/mdrun/md.cpp.o: dans la fonction «
> > > > > > PMPI::Cartcomm::Sub(bool const*) »:
> > > > > >
> > > > > >
> > > > >
> > > >
> > >
> >
> md.cpp:(.text._ZN4PMPI8Cartcomm3SubEPKb[_ZN4PMPI8Cartcomm3SubEPKb]+0x14b):undefined
> > > > > > reference to « MPI::Is_initialized() »
> > > > > >
> > > > > >
> > > > >
> > > >
> > >
> >
> CMakeFiles/mdrun_objlib.dir/mdrun/md.cpp.o:(.rodata._ZTVN3MPI2OpE[_ZTVN3MPI2OpE]+0x20):
> > > > > > undefined reference to « MPI::Op::Init(void (*)(void const*,
> void*,
> > > > int,
> > > > > > MPI::Datatype const&), bool) »
> > > > > >
> > > > > >
> > > > >
> > > >
> > >
> >
> CMakeFiles/mdrun_objlib.dir/mdrun/md.cpp.o:(.rodata._ZTVN3MPI2OpE[_ZTVN3MPI2OpE]+0x28):
> > > > > > undefined reference to « MPI::Op::Free() »
> > > > > >
> > > > > >
> > > > >
> > > >
> > >
> >
> CMakeFiles/mdrun_objlib.dir/mdrun/md.cpp.o:(.rodata._ZTVN3MPI2OpE[_ZTVN3MPI2OpE]+0x30):
> > > > > > undefined reference to « MPI::Op::Reduce_local(void const*,
> void*,
> > > int,
> > > > > > MPI::Datatype const&) const »
> > > > > >
> > > > > >
> > > > >
> > > >
> > >
> >
> CMakeFiles/mdrun_objlib.dir/mdrun/md.cpp.o:(.rodata._ZTVN3MPI2OpE[_ZTVN3MPI2OpE]+0x38):
> > > > > > undefined reference to « MPI::Op::Is_commutative() const »
> > > > > > collect2: erreur: ld a retourné 1 code d'état d'exécution
> > > > > > make[2]: *** [bin/mdrun_mpi] Erreur 1
> > > > > > make[1]: *** [src/programs/CMakeFiles/mdrun.dir/all] Erreur 2
> > > > > > make: *** [all] Erreur 2
> > > > > >
> > > > > > Maybe there is some missing link flags, I will keep digging in
> the
> > > mean
> > > > > > time.
> > > > > >
> > > > > > You mean, fill a bug to SGI or to Gromacs?
> > > > > >
> > > > >
> > > > > SGI's MPT header files should not define symbols that are not in
> the
> > > MPI
> > > > > spec - thus should not define UNDEFINED
> > > > >
> > > >
> > > > Looking at the header file, that's not the only one... There's plenty
> > of
> > > > them...
> > > >
> > > > Thanks,
> > > > Hubert
> > > >
> > > >
> > > >
> > > > >
> > > > > Mark
> > > > >
> > > > > Thanks,
> > > > > > Hubert
> > > > > >
> > > > > >
> > > > > > 2016-01-06 18:06 GMT+01:00 Mark Abraham <
> mark.j.abraham at gmail.com
> > >:
> > > > > >
> > > > > > > Hi,
> > > > > > >
> > > > > > > I suspect MPT has a bug such that one of its headers defines
> > > > UNDEFINED,
> > > > > > > which it should not do. If so, you can change
> > > > > > > src/gromacs/legacyheaders/names.h
> > > > > > > lines 110-1 to read
> > > > > > >
> > > > > > > #define GMX_UNDEFINED       "UNDEFINED"
> > > > > > > #define ENUM_NAME(e, max, names)  ((((e) < 0) || ((e) >=
> (max)))
> > ?
> > > > > > > GMX_UNDEFINED : (names)[e])
> > > > > > >
> > > > > > > and you should be fine. If so, please let us know, and please
> > file
> > > a
> > > > > bug
> > > > > > > report with SGI.
> > > > > > >
> > > > > > > Mark
> > > > > > >
> > > > > > > On Wed, Jan 6, 2016 at 5:33 PM hubert santuz <
> > > > hubert.santuz at gmail.com>
> > > > > > > wrote:
> > > > > > >
> > > > > > > > Hi everyone,
> > > > > > > >
> > > > > > > > I am trying to install the last version of Gromacs (5.1.1) on
> > our
> > > > SGI
> > > > > > > > cluster.
> > > > > > > > The mono-processor compilation went fine and now I would like
> > to
> > > > > > compile
> > > > > > > > the mdrun MPI version with the SGI MPT (the MPI library of
> SGI)
> > > > 2.09
> > > > > > > > (and also 2.12)
> > > > > > > > Here the cmake command I used:
> > > > > > > >
> > > > > > > > cmake .. -DGMX_GPU=OFF -DCMAKE_C_COMPILER=gcc
> > > > > > > >
> > > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > >
> > >
> >
> -DCMAKE_INSTALL_PREFIX=/opt/apps/software/pkg/gcc-4.9.0/mpt-2.0.9/gromacs/5.1.1/single
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > >
> > >
> >
> -DFFTWF_LIBRARY=/opt/apps/software/pkg/gcc-4.9.0/fftw/3.3.3/single/lib/libfftw3f.so
> > > > > > > >
> > > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > >
> > >
> >
> -DFFTWF_INCLUDE_DIR=/opt/apps/software/pkg/gcc-4.9.0/fftw/3.3.3/single/include
> > > > > > > >   -DGMX_MPI=ON
> > -DMPI_C_INCLUDE_PATH=/opt/sgi/mpt/mpt-2.12/include
> > > > > > > > -DMPI_C_LIBRARIES=/opt/sgi/mpt/mpt-2.12/lib/libmpi.so
> > > > > > > > -DGMX_BUILD_MDRUN_ONLY=ON  -DBUILD_SHARED_LIBS=off
> > > > > > > >
> > > > > > > >
> > > > > > > > The configuration went fine but when I ran make, I have the
> > > > following
> > > > > > > > error:
> > > > > > > >
> > > > > > > >
> > > > > > > > service0:gromacs-5.1.1/build # make
> > > > > > > > [  0%] Generating baseversion-gen.c
> > > > > > > > Scanning dependencies of target libgromacs
> > > > > > > > [  0%] Building C object
> > > > > > > >
> > > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > >
> > >
> >
> src/gromacs/CMakeFiles/libgromacs.dir/__/external/tng_io/src/compression/bwlzh.c.o
> > > > > > > > [...]
> > > > > > > > [  4%] Building CXX object
> > > > > > > >
> > > > > >
> > > >
> > src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o
> > > > > > > > [  4%] Building CXX object
> > > > > > > >
> > > > src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o
> > > > > > > > [  4%] Building CXX object
> > > > > > > >
> src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o
> > > > > > > > [  4%] Building CXX object
> > > > > > > > src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o
> > > > > > > > [  4%] Building CXX object
> > > > > > > >
> > > > >
> > src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o
> > > > > > > > [  4%] Building CXX object
> > > > > > > >
> > > src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_topology.cpp.o
> > > > > > > > [  4%] Building CXX object
> > > > > > > >
> src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o
> > > > > > > > In file included from
> > > > > > > >
> > > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > >
> > >
> >
> /opt/apps/software/src/gromacs/gromacs-5.1.1/src/gromacs/domdec/domdec_setup.cpp:53:0:
> > > > > > > >
> > > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > >
> > >
> >
> /opt/apps/software/src/gromacs/gromacs-5.1.1/src/gromacs/legacyheaders/names.h:110:25:
> > > > > > > > erreur: expected unqualified-id before string constant
> > > > > > > >   #define UNDEFINED       "UNDEFINED"
> > > > > > > >                           ^
> > > > > > > > make[2]: ***
> > > > > > > >
> > [src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o]
> > > > > > Erreur
> > > > > > > 1
> > > > > > > > make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all]
> > Erreur 2
> > > > > > > > make: *** [all] Erreur 2
> > > > > > > >
> > > > > > > > This is strange because, as I said, the mono-processor
> > > compilation
> > > > > went
> > > > > > > > fine.
> > > > > > > > I tried to upgrade the MPT library (2.12) without success.
> > > > > > > > I tried Openmpi 1.8.1 and it succeed.
> > > > > > > > Is there a compatibility issue with MPT ? I would like to
> keep
> > > this
> > > > > > > > library since I achieved better performance with it.
> > > > > > > >
> > > > > > > > Thanks,
> > > > > > > > Hubert
> > > > > > > > --
> > > > > > > > Gromacs Users mailing list
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