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

From: Mark Williamson <mjw.sdsc.edu>
Date: Mon, 10 May 2010 16:32:39 -0700

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 - 17:00:06 PDT
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