Re: [AMBER-Developers] sander.MPI tests randomly stall in Ubuntu 9.10

From: Lachele Foley <lfoley.ccrc.uga.edu>
Date: Mon, 10 May 2010 20:06:16 -0400

Having a nice set of commands is very good. Thanks, Mark! I think you posted them before. I'll save them somewhere. My issue is the time and not the knowledge, but this makes selling it to the student easier...

I tried "yum search gcc," which yielded the packages below, which I think are installed. It says "preview"... good enough if we get the mpi routines to point there?

gcc43.x86_64 : Preview of GCC version 4.3
gcc43-c++.x86_64 : C++ support for GCC version 4.3 preview
gcc43-gfortran.x86_64 : Fortran 95 support version 4.3 preview
gcc44.x86_64 : Preview of GCC version 4.4
gcc44-c++.x86_64 : C++ support for GCC version 4.4
gcc44-gfortran.x86_64 : Fortran support for GCC 4.4 preview
(etc.)

...on a hunch I found:

[root.aarya ~]# which gcc44
/usr/bin/gcc44
[root.aarya ~]# which g++44
/usr/bin/g++44
[root.aarya ~]# which gfortran44
/usr/bin/gfortran44

...and after some desperation, maybe this is it...

[root.aarya ~]# ls /usr/lib/gcc/x86_64-redhat-linux6E/
4.4.0


:-) Lachele

--
B. Lachele Foley, PhD '92,'02
Assistant Research Scientist
Complex Carbohydrate Research Center, UGA
706-542-0263
lfoley.ccrc.uga.edu
----- Original Message -----
From: Mark Williamson
[mailto:mjw.sdsc.edu]
To: AMBER Developers Mailing List
[mailto:amber-developers.ambermd.org]
Sent: Mon, 10 May 2010 19:32:39
-0400
Subject: Re: [AMBER-Developers] sander.MPI tests randomly stall in
Ubuntu 9.10
> Lachele Foley wrote:
> >> could you try different compiler?
> > 
> > On that machine?  Not easily, unless there's an rpm for it.  A new gcc
> from sources would take time I can't easily spare right now.  The student is
> pretty good... I can ask her.  Know of an rpm??  Sigh...
> 
> Hi Lachele, this is a little HowTo I use for building my own version of 
> gcc on a RHEL4 machine and may help here; you will need to adjust some 
> of the paths for your setup.
> 
> This mini-howto explains how to build the gnu compiler set on a RHEL4 
> x86_64 machine and how to set certain environment variables to enable 
> the fresh build to override existing gcc components.
> This process assumes gmp (GNU MP, a library for arbitrary precision
> arithmetic) has already been installed. This can be done as root using 
> this command:
> 
>          yum install gmp
> 
> 0) Get gcc 4.4.4:
>          wget ftp://mirrors.kernel.org/gnu/gcc/gcc-4.4.4/gcc-4.4.4.tar.bz2
> 
> 1) Untar it:
>          tar xfj gcc-4.4.4.tar.bz2
> 
> 2) Make a temp build directory at the same level in the directory tree 
> *and* change to it:
>          mkdir build ; cd build
> 
> 3) Run the gcc configure script *from* the temp build dir and tell it to 
> only build c, c++ and fortran and then where to put the built code 
> *after* the "make install" step:
> 
>          ../gcc-4.4.4/configure --enable-languages=c,c++,fortran 
> --prefix=/server-home/mjw/code/gcc/4.4.4
> 
> 4) Compile it; (the -j8 is to tell the make process to use 8 threads; I 
> have 8 cores on my compile machine; adjust to the number of cores on 
> your machine)
>          make -j8
> 
> 5) Wait for the compile to finish; this can take some time.
> 
> 6) Now that it is compiled, install it to the --prefix directory:
>          make install
> 
> 6b) Clean up the build directories and source... you don't need them now 
> and they are big (1.6G):
> 
>          cd .. ; rm -Rf build/ gcc-4.4.4
> 
> 7) Set the binary and library paths (This assumes you're running bash) 
> so that gcc 4.4.4 gets priority over existing gcc installs:
> 
>   export 
> LD_LIBRARY_PATH=/server-home/mjw/code/gcc/4.4.4/lib64:$LD_LIBRARY_PATH
>   export PATH=/server-home/mjw/code/gcc/4.4.4/bin:$PATH
>   export MANPATH=/server-home/mjw/code/gcc/4.4.4/man:$MANPATH
> 
> 8) Check that it has worked:
> [16:55][bunny:0.00][mjw:gcc]$ gfortran -v
> Using built-in specs.
> Target: x86_64-unknown-linux-gnu
> Configured with: ../gcc-4.4.4/configure
> --prefix=/server-home/mjw/code/gcc/4.4.4
> Thread model: posix
> gcc version 4.4.4 (GCC)
> 
> 9) Remember, you will need to set those environment variables if you 
> create new shell.
> 
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Received on Mon May 10 2010 - 17:30:02 PDT