HIi Ross,
After setting the two environment varible in .bashrc file and compiling it
by source command
no command is working on the terminal(such as vi, scp, cp, mv etc. etc.). I
don't understand what I will do. Please tell me.
$vi .bashrc
export MPI_HOME=/usr/local/mpich2-1.0.7-g95/
export PATH=/usr/local/mpich2-1.0.7-g95/bin/
$source .bashrc
Thank and regards
sudipta
On Sat, May 3, 2008 at 12:37 AM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Sudipta
>
> This is from the log file:
>
> configure:3475: gcc -static -all-static conftest.c >&5
> cc1: error: unrecognized command line option "-all-static"
>
> So that is the problem - thus try changing the export LDFLAGS=-all-static
> to
> just -static and try again.
>
> Good luck
> Ross
>
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
>
>
>
>
> From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf
> Of
> sudipta sinha
> Sent: Friday, May 02, 2008 11:30 AM
> To: amber.scripps.edu
> Subject: Re: AMBER: Installation problem of AMBER on cluster
>
> Hi Ross,
>
> Still I am getting some error during compilation of MPICH2. Here
> the issue is coming from c compiler. Now I clearly tell you what I have
> done.
> In .bashrc file we put the commands
> export FC=g95
> export F90=g95
> export LDFLAGS=-all-static
> export FFLAGS=-static
> export CFLAGS=-static
> export CXXFLAGS=-static
> export CXXLDFLAGS=-static
> and then compiled it by $source .bashrc
> Then I untar the file mpich2-1.0.7.tar.gz in /usr/local and also make a
> directory mpich2-1.0.7-g95 in /usr/local. Then I have typed the
> command
> $./configure –prefix=/usr/local/mpich2-1.0.7-g95
> But it is giving some errors
> ERRORS:==================================================
> Configuring MPICH2 version 1.0.7 with
> '--prefix=/usr/local/mpich2-1.0.7-g95/' 'CFLAGS=-static'
> 'CXXFLAGS=-static'
> 'F90=g95' 'FFLAGS=-static' 'LDFLAGS=-all-static'
> Running on system: Linux node3 2.6.9-67.ELsmp #1 SMP Wed Nov 7 13:56:44
> EST
> 2007 x86_64 x86_64 x86_64 GNU/Linux
> Executing mpich2prereq in /usr/local/mpich2-1.0.7/src/mpid/ch3 with
> Executing mpich2prereq in
> /usr/local/mpich2-1.0.7/src/mpid/ch3/channels/sock
> sourcing /usr/local/mpich2-1.0.7/src/pm/mpd/mpich2prereq
> sourcing /usr/local/mpich2-1.0.7/src/pm/mpd/setup_pm
> checking for gcc... gcc
> checking for C compiler default output file name... configure: error: C
> compiler cannot create executables
> See `config.log' for more details.
>
>
> ============================================================================
> =====
>
> I am also attaching the config.log file. Please see and tell me what is my
> wrong.
>
> Thanks and regards
> sudipta
> On Fri, May 2, 2008 at 9:11 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Sudipta,
>
> You should do the following if I remember correctly (assuming you are
> using
> the BASH shell):
>
> cd /usr/local
> tar –xvzf mpich2-1.0.7.tar.gz
> cd mpich2-1.0.7
> export FC=g95
> export F90=g95
> export LDFLAGS=-all-static
> export FFLAGS=-static
> export CFLAGS=-static
> export CXXFLAGS=-static
> export CXXLDFLAGS=-static
>
> (note: you may not need the last 5 options, or they may not work, but it
> is
> useful to try since if you can build a static version it will help you
> later
> since you will not need to worry about setting all the library paths on
> each
> node etc.)
>
> ./configure –prefix=/usr/local/mpich2-1.0.7-g95
>
> make
> make install
>
> (Then you can build the parallel version of AMBER – for amber 9)
>
> export MPI_HOME=/usr/local/mpich2-1.0.7-g95/
> export PATH=/usr/local/mpich2-1.0.7-g95/bin/
>
> (note: the two commands above should probably be put in the default bashrc
> so they get set every time you login.)
>
> cd $AMBERHOME/src/
> ./configure –static –mpich2 g95
> make clean
> make parallel
>
> Then you can run the parallel tests etc.
>
> Good luck,
> Ross
>
>
> From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf
> Of
> sudipta sinha
> Sent: Friday, May 02, 2008 12:39 AM
> To: amber.scripps.edu
> Subject: Re: AMBER: Installation problem of AMBER on cluster
>
> Dear sir,
>
> can you please help me about the compilation procedure of
> mpich2.
> We have installed our mpich2 by the following commands.
> cd /usr/local/
> tar -zxvf mpich2-1.0.7.tar.gz
> cd mpich2-1.0.7
> ./configure
> make
> make install
> Our operating system is RHEL4 and I think the default c and fortran
> compiler in RHEL4 are used during the compilation. Here we didn't set g95
> compiler for the compilation of mpich2. So, please guide me how to install
> mpich2 with g95 and gcc (default c compiler in RHEL4) compiler.
>
> sudipta
> On Fri, May 2, 2008 at 12:25 AM, David A. Case <case.scripps.edu> wrote:
> On Thu, May 01, 2008, sudipta sinha wrote:
> >
> > make clean
> >
> make: *** [clean] Error 2
>
> So, "make clean" did not work, because there is no config.h file.
> >
> > ./configure -mpich2 g95
>
> This step creates the config.h file. So, you need to do "make clean" now,
> (i.e. after the configure step).
> >
> > MPI_HOME is set to /usr/local/
> This implies that the mpich2 libraries (like libmpichf90.*) are in
> /usr/local/lib. Make sure that is the case.
>
> > evb_init.o(.data+0x460): undefined reference to
> `mpi_conversion_fn_null_'
> It seems to have found the libraries. The most common problem here is
> that
> the mpich2 libraries were compiled with a different fortran compiler than
> g95.
> Is that the case?
>
> ...good luck...dac
>
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Received on Sun May 04 2008 - 06:07:45 PDT
