Sorry to bother you again.
MPICH3.1.4 can be used for cpu-mpi version of amber16. However, the
cuda-mpi version of amber16 has problem to compile. The error information
are list below:
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are
deprecated, and may be removed in a future release (Use
-Wno-deprecated-gpu-targets to suppress warning).
make[5]: *** [kCalculateGBNonbondEnergy1.o] Hangup
make[1]: make: *** [cuda_parallel] Hangup*** [install] Hangup
make[4]: *** [cuda_dpfp_libs] Hangup
make[3]: *** [cuda_parallel_DPFP] Hangup
make[2]: *** [cuda_parallel] Hangup
2016-10-18 22:47 GMT+08:00 Daniel Roe <daniel.r.roe.gmail.com>:
> Hi,
>
> On Tue, Oct 18, 2016 at 10:24 AM, jacky zhao <jackyzhao010.gmail.com>
> wrote:
> >
> > /home/user/amber16/lib/libfftw3_mpi.so: undefined reference to
> > `ompi_mpi_char'
>
> These kinds of errors during the link step usually happen when you
> change compiler types/versions and old libraries get leftover. You may
> want to try running a 'make uninstall' and then re-running configure.
>
> -Dan
>
> PS - The patch will be ready to go soon.
>
> >
> > /home/user/amber16/lib/libfftw3_mpi.so: undefined reference to
> > `MPI_Comm_f2c'
> >
> > /home/user/amber16/lib/libfftw3_mpi.so: undefined reference to
> > `ompi_mpi_int'
> >
> > /home/user/amber16/lib/libfftw3_mpi.so: undefined reference to
> > `ompi_mpi_comm_null'
> >
> > /home/user/amber16/lib/libfftw3_mpi.so: undefined reference to
> > `ompi_mpi_op_max'
> >
> > /home/user/amber16/lib/libfftw3_mpi.so: undefined reference to
> > `ompi_mpi_op_lor'
> >
> > /home/user/amber16/lib/libfftw3_mpi.so: undefined reference to
> > `ompi_mpi_op_land'
> >
> > /home/user/amber16/lib/libfftw3_mpi.so: undefined reference to
> > `ompi_mpi_unsigned'
> >
> > /home/user/amber16/lib/libfftw3_mpi.so: undefined reference to
> > `ompi_mpi_double'
> >
> > /home/user/amber16/lib/libfftw3_mpi.so: undefined reference to
> > `ompi_mpi_unsigned_long'
> >
> > /home/user/amber16/lib/libfftw3_mpi.so: undefined reference to
> > `ompi_mpi_op_sum'
> >
> > collect2: error: ld returned 1 exit status
> >
> > make[2]: *** [/home/user/amber16/bin/mdgx.MPI] Error 1
> >
> > make[2]: Leaving directory `/home/user/amber16/AmberTools/src/mdgx'
> >
> > make[1]: *** [parallel] Error 2
> >
> > make[1]: Leaving directory `/home/user/amber16/AmberTools/src'
> >
> > make: *** [install] Error 2
> >
> >
> > 2016-10-18 22:02 GMT+08:00 jacky zhao <jackyzhao010.gmail.com>:
> >
> >> MPICH3.2:
> >>
> >>
> >> mpicxx -Wall -Wno-unused-function -c -I/home/user/amber16/include -O3
> >> -mtune=native -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
> -DBINTRAJ
> >> -DHASGZ -DHASBZ2 -D__PLUMED_HAS_DLOPEN -DMPI
> >> -I/home/user/amber16/include -DUSE_SANDERLIB -o FileIO_Gzip.o
> >> FileIO_Gzip.cpp
> >>
> >> mpicxx -Wall -Wno-unused-function -c -I/home/user/amber16/include -O3
> >> -mtune=native -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
> -DBINTRAJ
> >> -DHASGZ -DHASBZ2 -D__PLUMED_HAS_DLOPEN -DMPI
> >> -I/home/user/amber16/include -DUSE_SANDERLIB -o FileIO_Mpi.o
> >> FileIO_Mpi.cpp
> >>
> >> FileIO_Mpi.cpp: In member function 'virtual int
> FileIO_Mpi::Seek(off_t)':
> >>
> >> FileIO_Mpi.cpp:33:28: error: 'SEEK_SET' was not declared in this scope
> >>
> >> if (pfile_.Fseek(offset, SEEK_SET)) return 1;
> >>
> >> ^
> >>
> >> FileIO_Mpi.cpp: In member function 'virtual int FileIO_Mpi::Rewind()':
> >>
> >> FileIO_Mpi.cpp:39:24: error: 'SEEK_SET' was not declared in this scope
> >>
> >> if (pfile_.Fseek(0L, SEEK_SET)) return 1;
> >>
> >> ^
> >>
> >> make[4]: *** [FileIO_Mpi.o] Error 1
> >>
> >> make[4]: Leaving directory `/home/user/amber16/
> AmberTools/src/cpptraj/src'
> >>
> >> make[3]: *** [parallel] Error 2
> >>
> >> make[3]: Leaving directory `/home/user/amber16/AmberTools/src/cpptraj'
> >>
> >>
> >> 510,1
> >>
> >> 2016-10-18 22:01 GMT+08:00 jacky zhao <jackyzhao010.gmail.com>:
> >>
> >>> Very well for this good news.
> >>> .Case I have used MPICH3.2 to compile cpu-mpi version of amber16, but
> >>> the same error occur. As your suggestion, I am using MPICH3.1.4 to
> >>> recompile it.
> >>>
> >>>
> >>> 2016-10-18 21:22 GMT+08:00 Daniel Roe <daniel.r.roe.gmail.com>:
> >>>
> >>>> In addition to Dave's suggestions, I am currently working on a patch
> >>>> to AmberTools that addresses this. Should be out today or tomorrow.
> >>>>
> >>>> -Dan
> >>>>
> >>>> On Tue, Oct 18, 2016 at 9:08 AM, David A Case <david.case.rutgers.edu
> >
> >>>> wrote:
> >>>> > On Tue, Oct 18, 2016, jacky zhao wrote:
> >>>> >
> >>>> >> open-mpi version is 2.0.1. and open-mpi example test is passed.
> >>>> >> I have used open-mpi to compile cuda and cuda.mpi verion of amber16
> >>>> without
> >>>> >> any problems. But error was encountered in the cpu-mpi version of
> >>>> amber16.
> >>>> >> The information are list below:
> >>>> >>
> >>>> >>
> >>>> >> if (pfile_.Fseek(offset, SEEK_SET)) return 1;
> >>>> >>
> >>>> >> FileIO_Mpi.cpp: In member function 'virtual int
> FileIO_Mpi::Rewind()':
> >>>> >> FileIO_Mpi.cpp:39:24: error: 'SEEK_SET' was not declared in this
> scope
> >>>> >> if (pfile_.Fseek(0L, SEEK_SET)) return 1;
> >>>> >> ^
> >>>> >
> >>>> > Option 1: use an older version of OpenMPI.
> >>>> > Option 2: use the patch suggested below, or get the github version
> of
> >>>> > OpenMPI
> >>>> > Option 3: use a different MPI, say mpich2
> >>>> >
> >>>> > See these previous posts:
> >>>> >
> >>>> > http://archive.ambermd.org/201610/0109.html
> >>>> >
> >>>> > ...dac
> >>>> >
> >>>> > _______________________________________________
> >>>> > AMBER mailing list
> >>>> > AMBER.ambermd.org
> >>>> > http://lists.ambermd.org/mailman/listinfo/amber
> >>>>
> >>>>
> >>>>
> >>>> --
> >>>> -------------------------
> >>>> Daniel R. Roe
> >>>> Laboratory of Computational Biology
> >>>> National Institutes of Health, NHLBI
> >>>> 5635 Fishers Ln, Rm T900
> >>>> Rockville MD, 20852
> >>>> https://www.lobos.nih.gov/lcb
> >>>>
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>
> >>>
> >>>
> >>>
> >>> --
> >>> Lei Zhao, Ph.D.
> >>> International Joint Cancer Institute of the Second Military Medical
> >>> University
> >>> National Engineering Research Center for Antibody Medicine
> >>> New Library Building 11th floor,800 Xiang Yin Road
> >>> Shanghai 200433
> >>> P.R.China
> >>>
> >>
> >>
> >>
> >> --
> >> Lei Zhao, Ph.D.
> >> International Joint Cancer Institute of the Second Military Medical
> >> University
> >> National Engineering Research Center for Antibody Medicine
> >> New Library Building 11th floor,800 Xiang Yin Road
> >> Shanghai 200433
> >> P.R.China
> >>
> >
> >
> >
> > --
> > Lei Zhao, Ph.D.
> > International Joint Cancer Institute of the Second Military Medical
> > University
> > National Engineering Research Center for Antibody Medicine
> > New Library Building 11th floor,800 Xiang Yin Road
> > Shanghai 200433
> > P.R.China
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Lei Zhao, Ph.D.
International Joint Cancer Institute of the Second Military Medical
University
National Engineering Research Center for Antibody Medicine
New Library Building 11th floor,800 Xiang Yin Road
Shanghai 200433
P.R.China
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Received on Tue Oct 18 2016 - 09:30:02 PDT
