David van der Spoel wrote:
Nicolas Sapay wrote:
David van der Spoel wrote:
Nicolas Sapay wrote:
David van der Spoel wrote:
Nicolas Sapay wrote:
Hi,
I'm trying to compile the Gromacs-3.3.3 package with MPI and have
the following issue when I run the configuration script:
./configure --prefix /home/users/nsapay/local/bin/gromacs-3.3.3
--program-suffix _mpi --enable-mpi --disable-nice MPICC=mpicc
CC=gcc
--without-x
CPPFLAGS=-I/home/users/nsapay/local/bin/fftw-3.1.2/include/
LDFLAGS=-L/home/users/nsapay/local/bin/fftw-3.1.2/lib/
>>> checking size of int... configure: error: cannot compute
sizeof
(int)
the config.log file tells me it's because a MPI library is not
found:
configure:7621: mpicc -o conftest -O3 -fomit-frame-pointer
-finline-functions -Wall -Wno-unused -funroll-all-loops
-I/home/users/nsapay/local/bin/fftw-3.1.2/include/
-L/opt/hpmpi/lib/linux_amd64/
-L/home/users/nsapay/local/bin/fftw-3.1.2/lib/ conftest.c >&5
configure:7624: $? = 0
configure:7630: ./conftest
./conftest: error while loading shared libraries: libmpio.so.1:
cannot open shared object file: No such file or directory
configure:7633: $? = 127
configure: program exited with status 127
It seems that the crux is up here. Is there a libmpio.so.1 on your
system? If so, where? Why isn't it found? Could it be that you have to
source some scripts before compiling and running stuff?
The library is in the directory "/opt/hpmpi/lib/linux_amd64/". Is is
appears in command line for the compilation of conftest, but this
directory do not seem to be correctly included in my environment. I'll
ask the system administrator of the cluster. I may need to export a
variable or load a module...
I tried to reconfigure the installation by including the
directory where the libmpi is stored:
./configure --prefix /home/users/nsapay/local/bin/gromacs-3.3.3
--program-suffix _mpi --enable-mpi --disable-nice MPICC=mpicc
CC=gcc --without-x
CPPFLAGS=-I/home/users/nsapay/local/bin/fftw-3.1.2/include/
LDFLAGS="-L/opt/hpmpi/lib/linux_amd64/
-L/home/users/nsapay/local/bin/fftw-3.1.2/lib/"
You might want to try
LD=mpicc
Nope, same error...
You may need to add fftw library path to ldflags as well.
I did, but the error is still related to libmpi... Actually, I
realize there is this error few lines above:
configure:5488: mpicc -E
-I/home/users/nsapay/local/bin/fftw-3.1.2/include/ conftest.c
conftest.c:18:28: ac_nonexistent.h: No such file or directory
configure:5494: $? = 1
So, there might be something wrong with the conftest compilation
itself... But the way, shouldn't conftest be run with "mpirun
./conftest" rather that just "./conftest"? I'm really not a mpicc
monk. It's just an intuition
But it doesn't work. I get exactly the same error message. Why
the libmpio.so.1 library is not recognized by the configuration
script? Note that I have compiled Gromacs without MPI with no
particular issue. The system is a HP cluster with AMD
processors, Red Hat 4.5, gcc/mpicc 3.4.6.
Thanks a lot for your advices
-Nicolas
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begin:vcard
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