[maker-devel] Problem Installing with opencc

[Carson Holt]

MAKER installation doesn't have a Makefile.PL.  The parameters  for
compilation of the MPI bindings are being set by mpicc itself, Perl, or
environmental variables on your system.  In general you want both Perl and
OpenMPI to be compiled by the same compiler or you can get cross library
problems (as Perl is using the shared libraries in OpenMPI so all
communication is really at the C level).  This is not always the case, but
can happen (I have been fine for the most part mixing pgi, intel, and gcc
compiled OpenMPI, but have never tried open64 compilers).

Alternatively you can try manually setting the values in the following
environmental variables before installing MAKER which should affect the
parameter settings (this means before even running the 'perl Build.PL'
step):

LDFLAGS=
LDDLFLAGS=
CCCDLFLAGS=
CCDLFLAGS=

Also you need to export the following variable for OpenMPI to work with
shared libraries before trying to install MAKER or run MAKER (this means
before even running the 'perl Build.PL' step).  It's best just to add it to
your ~/.bashrc or ~/.bash_profile.

export LD_PRELOAD=/share/apps/openmpi/OpenMPI-1.6.3/lib/libmpi.so

You will need to run 'source ~/.bashrc' or 'source ~/.bash_profile' after
adding it to implement the changes into the current terminal session.

Thanks,
Carson



From:  Alex Sickler <sickler.alex at gmail.com>
Date:  Wednesday, 12 June, 2013 2:22 PM
To:  <maker-devel at yandell-lab.org>
Cc:  <sicklaj10 at juniata.edu>
Subject:  [maker-devel] Problem Installing with opencc

Hi all,

I am trying to install Maker 2.28. When I go to install Maker, it gives the
following error message:

/usr/bin/perl /usr/local/share/perl5/ExtUtils/xsubpp  -typemap
"/usr/share/perl5/ExtUtils/typemap"   MPI.xs $
/share/apps/openmpi/OpenMPI-1.6.3/bin/mpicc -c  -I"/share/apps/maker/src"
-I/share/apps/openmpi/OpenMPI-1.6.3/include -D_REENTRANT -D_GNU_SOUR$
opencc WARNING: unknown flag: -fstack-protector
opencc WARNING: unknown flag: -fstack-protector
opencc ERROR: -- not allowed in non XPG4 environment
opencc ERROR parsing --param=ssp-buffer-size=4: unknown flag
make: *** [MPI.o] Error 2

The to everything is correct. I tried looking in the Makefile.PL but could
not find the "param=" option.


Any help is greatly appreciated,
Alex
_______________________________________________ maker-devel mailing list
maker-devel at box290.bluehost.com
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20130613/2a28c110/attachment-0003.html>