Compiling ABySS with MPICH

[Alden Huang]

Hi,

I am trying to install abyss locally on the DIAG cluster (http://diagcomputing.org/), which coincidentally has your program improperly installed.

Basically, I am unable to build ABySS version 1.5.2 with MPICH support; the program configures fine but ABYSS-P is never made.

## Here is the compile command I am running:

./configure --enable-mpich CPPFLAGS="-I/diag/home/alden/local/include -I/usr/mpi/gcc/mvapich-1.2.0/include" --with-mpi=/usr/lib64/mpich2/lib --prefix=/diag/home/alden/local

# mpi.h is located in /usr/mpi/gcc/mvapich-1.2.0/include

## Here are (what i think) are the relevant output from running .configure

checking mpi.h usability... yes
checking mpi.h presence... yes
checking for mpi.h... yes
checking for MPI_Init in -lmpich... no

## Here is the output from mpichversion

MPICH Version:        1.2.7
MPICH Release date:    $Date: 2005/06/22 16:33:49$
MPICH Patches applied:    none
MPICH configure:     --enable-sharedlib --with-device=ch_gen2 --with-arch=LINUX --prefix=/var/tmp/OFED_topdir/BUILDROOT/mvapich_gcc-1.2.0-3635.x86_64/usr/mpi/gcc/mvapich-1.2.0 --enable-f77 --enable-f90 -lib=-L/usr/lib64 -libverbs -libumad -lpthread -Wall
MPICH Device:        ch_gen2

I checked the message board pretty thoroughly, but all of them are specific for openmpi...

Any help or pointers you could give would be greatly appreciated.

Thanks, and thanks for the program (runs great on my lab cluster, just not enough RAM =).

alden

[Ben Vandervalk]

Hi Alden,

Try "--with-mpi=/usr/lib64/mpich2" instead.  The "--with-mpi" option expects a directory that contains subdirectories called "include" and "lib".   If that doesn't work, have a look in "config.log" to see if you can figure what went wrong during the check for MPI_Init.

If you can't see what that the problem is, send me your config.log file and maybe I can help.

- Ben

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[Alden Huang]

Hi Ben,

Actually I realized my error and already did as you suggested...but unfortunately it didn't work.

I'm attaching my config.log, but it still cant find MPICH:

configure:6835: checking for MPI_Init in -lmpich
configure:6860: gcc -o conftest -g -O2 -I/diag/home/alden/abyss-1.5.2  -isystem/usr/lib64/mpich2/include  -I/diag/home/alden/local/include -I/usr/mpi/gcc/mvapich-1.2.0/include -isystem/diag/home/alden/abyss-1.5.2/boost_1_55_0 -L/usr/lib64/mpich2/lib   conftest.c -lmpich  -lpthread  >&5
/usr/bin/ld: cannot find -lmpich

I guess the system is using modules to load environment variables, so I tried loading the mpich module but still, no luck.

Any suggestions or advice on things to try would be appreciated...

Thanks for the reply!

~alden

[Ben Vandervalk]

Hi Alden,

I noticed that when I looked in the output of "./configure --help" that there is an option called "--enable-mpich".  Could you try adding that to your configure line and see if it solves the problem?

It looks like "./configure" is searching for a file called "libmpich.so" in /usr/lib64/mpich2/lib and not finding it.

You might also try setting the LIBRARY_PATH environment variable:

$ export LIBRARY_PATH=/usr/lib64/mpich2/lib:$LIBRARY_PATH

which tells gcc to additionally look in /usr/lib64/mpich2/lib when searching for libraries.  If that works, you also need to set

$ export LD_LIBRARY_PATH=/usr/lib64/mpich2/lib:$LD_LIBRARY_PATH

prior to running the compiled binaries.  (LIBRARY_PATH tells gcc where to look for libraries when compiling programs and LD_LIBRARY_PATH tells the system where to search for libraries required by programs.)
  
- Ben

[Joel Shore]

HI Alden,

 Did you ever get abyss running on the DIAG cluster?

If so, I'd greatly appreciate any advice on how to use it there.

At the moment, I keep being told the ABYSS-P executable isn't found

Thanks

Joel