I have used MPICH3.1.4 to compile cpu-mpi version of amber16, the error
information are list below:
mpicc -O3 -mtune=native -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-DBINTRAJ -DHASGZ -DHASBZ2 -D__PLUMED_HAS_DLOPEN -DMPI \
-o /home/user/amber16/bin/mdgx.MPI CompFrc.o BSpline.o Grid.o Random.o
mdgxVector.o Matrix.o ChargeMap.o pmeRecip.o mleRecip.o pmeDirect.o
CrdManip.o CellManip.o Topology.o Trajectory.o SpecialMath.o Nonbonded.o
Bonded.o Parse.o Command.o Constraints.o Thermostats.o Barostats.o
Integrator.o Timings.o Manual.o VirtualSites.o Buckingham.o ThermoDyn.o
ChargeFit.o ParamOut.o ParamRead.o ParamFit.o IPolQ.o Restraints.o Debug.o
BroadcastCommand.o MPIMap.o MPITypeCast.o ptrajmask.o AmberNetcdf.o mdgx.o
-L/home/user/amber16/lib -larpack -llapack -lblas -lfftw3_mpi -lfftw3
/home/user/amber16/lib/libnetcdf.a -lm
/home/user/amber16/lib/libfftw3_mpi.so: undefined reference to
`ompi_mpi_char'
/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
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Received on Tue Oct 18 2016 - 07:30:04 PDT
