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
Received on Tue Oct 18 2016 - 08:00:03 PDT
