AMBER Archive (2008)

Subject: RE: AMBER: Installation problem of AMBER on cluster

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Fri May 02 2008 - 16:33:48 CDT

export PATH=/usr/local/mpich2-1.0.7-g95/bin/

--->

export PATH=/usr/local/mpich2-1.0.7-g95/bin/:$PATH

Sorry about that - busy day....

All the best
Ross

> -----Original Message-----
> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
> Of Ross Walker
> Sent: Friday, May 02, 2008 2:19 PM
> To: amber_at_scripps.edu
> Subject: RE: AMBER: Installation problem of AMBER on cluster
>
> Hi Sudipta
>
> Did you replace the contents of ~/.bashrc with those two exports?
>
> You need to append these to your ~/.bashrc file. It should look something
> like:
>
> # .bashrc
> # User specific aliases and functions
> # Source global definitions
> if [ -f /etc/bashrc ]; then
> . /etc/bashrc
> fi
> #default create 0700
> umask 077
> #CVS Specs
> export MPI_HOME=/usr/local/mpich2-1.0.7-g95/
> export PATH=/usr/local/mpich2-1.0.7-g95/bin/
>
> I suggest though that you find someone else who has a username on the
> machine and see what their default .bashrc file looks like. Do you have a
> system administrator? Someone who set the machine up for you?
>
> Ross
>
> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
> Of
> sudipta sinha
> Sent: Friday, May 02, 2008 1:30 PM
> To: amber_at_scripps.edu
> Subject: Re: AMBER: Installation problem of AMBER on cluster
>
> 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_at_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_at_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_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
> Of
> sudipta sinha
> Sent: Friday, May 02, 2008 11:30 AM
> To: amber_at_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_at_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_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
> Of
> sudipta sinha
> Sent: Friday, May 02, 2008 12:39 AM
> To: amber_at_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_at_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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