.Ucisik: I can reproduce your error. So while waiting for a fix
(hopefully), you can either follow suggestions from Marcelo or Alican.
You can also turn off cpptraj build with mpi in AmberTools/src/Makefile
(search for *cpptraj::* and comment related lines)
cheers
Hai
On Mon, Oct 10, 2016 at 2:02 PM, Gulsevin,Alican <agulsevin.chem.ufl.edu>
wrote:
> >From what I understand, the problem is that C and OpenMPI libraries can
> have overlapping stdio.h variables. Therefore, variables can mean different
> things within their "scope" for some OpenMPI (and mpich) versions. The
> older version suggested by Marcelo can work. If not, you can try the
> version suggested by Amber itself.
>
> Best,
> Alican
>
> ________________________________________
> From: Marcelo Andrade Chagas <andrade.mchagas.gmail.com>
> Sent: Monday, October 10, 2016 1:53 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] AmberTools16 Installation with openMPI fails?
>
> Dear,
>
> I found a problem once with the version of MPI.
>
> I managed to solve using this:
>
> openmpi-1.6.5.tar.gz
>
> It seems to have some bivliotecas files that were modified in the latest
> versions and amber during the build does not find the necessary libraries.
>
> Best regards
>
> Marcelo Andrade Chagas, MSc
> (PhD student)
> Laboratório de Química Computacional e Modelagem Molecular - LQC-MM
> * http://lqcmm.qui.ufmg.br/
> Departamento de Química da Universidade Federal de Minas Gerais - UFMG
> Tel:(31)3409-5776
>
> 2016-10-10 14:39 GMT-03:00 Ucisik, Melek Nihan <ucisik.illinois.edu>:
>
> > Hello,
> >
> > I wanted to follow up on this. I started over clean and did the serial
> > installation first. No problems there. Using openMPI version 2.0.1, I
> > attempted the parallel installation. mpif90, mpicc, mpiexec, and mpirun
> > are all pointing to the correct directory.
> >
> > echo $PATH
> > /opt/amber16/16.14/amber16/bin:/opt/amber16/16.14/
> > amber16/bin:/opt/amber16/16.14/amber16/bin:/opt/amber16/
> > 16.14/amber16/bin:/opt/openmpi/2.0.1/bin:/opt/pkg-
> > config/0.28/bin:/opt/python/2.7/bin:/usr/local/brl/bin:/usr/
> > lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/
> > sbin:/usr/sbin:/sbin:/home/cddadmin/bin:/opt/openmpi/2.0.1/include
> >
> > echo $LD_LIBRARY_PATH
> > /opt/amber16/16.14/amber16/lib:/opt/amber16/16.14/
> > amber16/lib:/opt/amber16/16.14/amber16/lib:/opt/amber16/
> > 16.14/amber16/lib:/opt/openmpi/2.0.1:/opt/openmpi/2.
> > 0.1/lib:/opt/python/2.7/lib:/usr/local/brl/local/lib:/usr/
> > local/brl/local/lib64:
> >
> > make clean
> > ./configure --with-python /opt/python/2.7/bin/python -mpi gnu
> > make install
> >
> > Same errors as before showed up:
> >
> > FileIO_Mpi.cpp: In member function ‘virtual int FileIO_Mpi::Seek(off_t)’:
> > FileIO_Mpi.cpp:33: error: ‘SEEK_SET’ was not declared in this scope
> > FileIO_Mpi.cpp: In member function ‘virtual int FileIO_Mpi::Rewind()’:
> > FileIO_Mpi.cpp:39: error: ‘SEEK_SET’ was not declared in this scope
> > make[4]: *** [FileIO_Mpi.o] Error 1
> > make[4]: Leaving directory `/usr/local/brl/opt/amber16/
> > 16.14/amber16/AmberTools/src/cpptraj/src'
> > make[3]: *** [parallel] Error 2
> > make[3]: Leaving directory `/usr/local/brl/opt/amber16/
> > 16.14/amber16/AmberTools/src/cpptraj'
> > make[2]: *** [cpptraj] Error 2
> > make[2]: Leaving directory `/usr/local/brl/opt/amber16/
> > 16.14/amber16/AmberTools/src'
> > make[1]: *** [parallel] Error 2
> > make[1]: Leaving directory `/usr/local/brl/opt/amber16/
> > 16.14/amber16/AmberTools/src'
> > make: *** [install] Error 2
> >
> >
> > Could this be a bug? The FileIO_Mpi.cpp at $AMBERHOME/AmberTools/src/
> cpptraj/src
> > seems to be the problem. Any ideas? I can’t get past this point.
> >
> > Thanks,
> >
> > M. Nihan Ucisik
> >
> >
> > On Oct 8, 2016, at 11:56 AM, Ucisik, Melek Nihan <ucisik.illinois.edu
> > <mailto:ucisik.illinois.edu>> wrote:
> >
> > Hi,
> >
> > I did build the serial first with no problems and I did use the normal
> > configure script with the -mpi gnu flag after having checked where the
> > mpif90 and mpirun were pointing. They point to the same openmpi
> > installation which is in my path.
> >
> > “Make install” gave errors after using the normal configure script which
> > is why I tried the configure_openmpi script. I thought the configure step
> > failed with the normal script. Here are the errors I had gotten:
> >
> > FileIO_Mpi.cpp: In member function ‘virtual int FileIO_Mpi::Seek(off_t)’:
> > FileIO_Mpi.cpp:33: error: ‘SEEK_SET’ was not declared in this scope
> > FileIO_Mpi.cpp: In member function ‘virtual int FileIO_Mpi::Rewind()’:
> > FileIO_Mpi.cpp:39: error: ‘SEEK_SET’ was not declared in this scope
> > make[4]: *** [FileIO_Mpi.o] Error 1
> > make[4]: Leaving directory `/usr/local/brl/opt/amber16/
> > 16.14/AmberTools/src/cpptraj/src'
> > make[3]: *** [parallel] Error 2
> > make[3]: Leaving directory `/usr/local/brl/opt/amber16/
> > 16.14/AmberTools/src/cpptraj'
> > make[2]: *** [cpptraj] Error 2
> > make[2]: Leaving directory `/usr/local/brl/opt/amber16/
> > 16.14/AmberTools/src'
> > make[1]: *** [parallel] Error 2
> > make[1]: Leaving directory `/usr/local/brl/opt/amber16/
> > 16.14/AmberTools/src'
> > make: *** [install] Error 2
> >
> > I know this is some kind of openmpi/path problem but I wasn’t able to get
> > it resolved as I am checking everything and nothing seems out of place in
> > terms of paths etc. Another issue is that “make clean” gives an error
> also:
> >
> > make[1]: Entering directory `/usr/local/brl/opt/amber16/16.14/src'
> > make[1]: *** No rule to make target `clean'. Stop.
> > make[1]: Leaving directory `/usr/local/brl/opt/amber16/16.14/src'
> > make: [clean] Error 2 (ignored)
> >
> > I guess I’ll try to start over. I had installed Amber multiple times
> > before (thanks to Jason’s wiki) on different platforms and didn’t have
> > these problems, so I am confused as to what is going wrong this time.
> >
> > Anyway, thanks for the suggestions,
> >
> > Nihan
> >
> >
> > On Oct 7, 2016, at 5:30 PM, Charles Lin <clin92.ucsd.edu<mailto:clin92
> > .ucsd.edu><mailto:clin92.ucsd.edu>> wrote:
> >
> > Check if your mpif90 and mpirun point to the right executables.
> >
> > (which mpif90 and which mpirun).
> >
> > You should theoretically be able to use the normal configure script for
> > this.
> >
> > Charlie
> > ________________________________________
> > From: Ucisik, Melek Nihan [ucisik.illinois.edu<mailto:uc
> isik.illinois.edu
> > ><mailto:ucisik.illinois.edu>]
> > Sent: Friday, October 07, 2016 3:23 PM
> > To: AMBER Mailing List
> > Subject: [AMBER] AmberTools16 Installation with openMPI fails?
> >
> > Hi,
> >
> > I am trying to install AmberTools using openMPI. I did have the
> > openmpi-2.0.1 module loaded before I started with the installation, so I
> > had mpicc and mpif90 in my path. I tried using the “configure_openmpi”
> > script as suggested in the manual and it failed multiple times, so I
> tried
> > tweaking it. The script advised me to have the openmpi directory also at
> > $AMBERHOME/AmberTools/src, so I copied openmpi-2.0.1.tar.bz2 to there and
> > extracted. I modified the configure_openmpi script in the line where
> > “mpidirs” is defined. I ended up with this:
> >
> > “./configure_openmpi: line 119: YACC=/opt/amber16/16.14/bin/yacc: No
> such
> > file or directory
> > openmpi configure failed, returning 127“
> >
> > This made no sense to me because /opt/amber16/16.14/bin/yacc was there.
> >
> > Then I removed the “$static” variable from line 119 of configure_openmpi
> > and this is what I got:
> >
> > "configure: error: /bin/sh config/config.sub failed
> > openmpi configure succeeded.
> > (You may need to add /opt/amber16/16.14/lib to your LD_LIBRARY_PATH)
> > make: *** No rule to make target `clean'. Stop.
> > make: *** No rule to make target `install'. Stop.”
> >
> > So I am confused about this outcome because it says “error" in one line
> > and “succeeded" in the next.
> >
> > Could someone tell me if I am good to continue from this point? Did the
> > configuration fail or succeed?
> >
> > Thanks,
> >
> >
> > M. Nihan Ucisik
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org<mailto:AMBER.ambermd.org><mailto:AMBER.ambermd.org>
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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> >
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Received on Mon Oct 10 2016 - 11:30:03 PDT
