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:ucisik.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
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Received on Mon Oct 10 2016 - 11:00:02 PDT
