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Old 02-03-2010, 04:25 PM
Jon Forrest
 
Default Updating gfortran in CentOS 5.4?

We're finding that several of the packages we
need don't compile using the version 4.1.2 of
gfortran that comes with CentOS 5.4. So,
I've built the latest version of gfortran (e.g. 4.4.2)
but I've done it so that all the new version's
files go in /share/apps/gnu so that they
don't interfere with the standard gcc distribution
(building gfortran requires building some parts
of gcc).

Although I can compile and run a simple fortran
"Hello, world" program using the version of
gfortran I built this way, trying to run a
more complex application, such as charmm (a molecular
dynamics program), fails. When I run charmm, I get the
message "Killed".

Running strace ./charmm shows

execve("./charmm", ["./charmm"], [/* 43 vars */] <unfinished ...>
+++ killed by SIGKILL

Since "Hello, world" compiles and runs, but charmm
compiles and doesn't run, there's something wrong
with how charmm is linked. Also, although the
'file charmm' command shows an ELF 64-bit dynamically
linked file, 'ldd charmm' says " not a dynamic executable"
(note no file name). So, something is strange.

What have other people done about building new versions
of gfortran on CentOS 5.4? Is this worth the trouble?
Or, is it better to just go with Intel Fortran?

Cordially,
--
Jon Forrest
Research Computing Support
College of Chemistry
173 Tan Hall
University of California Berkeley
Berkeley, CA
94720-1460
510-643-1032
jlforrest@berkeley.edu

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Old 02-03-2010, 05:03 PM
Akemi Yagi
 
Default Updating gfortran in CentOS 5.4?

On Wed, Feb 3, 2010 at 9:25 AM, Jon Forrest <jlforrest@berkeley.edu> wrote:

> Although I can compile and run a simple fortran
> "Hello, world" program using the version of
> gfortran I built this way, trying to run a
> more complex application, such as charmm (a molecular
> dynamics program), fails. When I run charmm, I get the
> message "Killed".

Regarding the compilation question, you may want to try the CHARMM forums at:

http://www.charmm.org/ubbthreads/ubbthreads.php?ubb=cfrm

I could ask around at my work place (one of the developers used to
work here), but it will probably be much quicker if you use the
forums.

Akemi
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Old 02-03-2010, 05:38 PM
 
Default Updating gfortran in CentOS 5.4?

> We're finding that several of the packages we
> need don't compile using the version 4.1.2 of
> gfortran that comes with CentOS 5.4. So,
> I've built the latest version of gfortran (e.g. 4.4.2)
> but I've done it so that all the new version's
> files go in /share/apps/gnu so that they
> don't interfere with the standard gcc distribution
> (building gfortran requires building some parts
> of gcc).
<snip>
> Since "Hello, world" compiles and runs, but charmm
> compiles and doesn't run, there's something wrong
> with how charmm is linked. Also, although the
> 'file charmm' command shows an ELF 64-bit dynamically
> linked file, 'ldd charmm' says " not a dynamic executable"
> (note no file name). So, something is strange.
<snip>
I was just talking to one of the researchers here who's built it, and
pointed out the completely obvious (once he pointed it out): the "<blank>
not a dynamic executable" tells you that that piece, at least, is
statically linked, *not* dynamic. He recommends getting a core dump, so
you can do a traceback.

mark





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Old 02-03-2010, 05:49 PM
Tony Schreiner
 
Default Updating gfortran in CentOS 5.4?

On Feb 3, 2010, at 12:25 PM, Jon Forrest wrote:

> We're finding that several of the packages we
> need don't compile using the version 4.1.2 of
> gfortran that comes with CentOS 5.4. So,
> I've built the latest version of gfortran (e.g. 4.4.2)
> but I've done it so that all the new version's
> files go in /share/apps/gnu so that they
> don't interfere with the standard gcc distribution
> (building gfortran requires building some parts
> of gcc).


..

There is also a gcc44-gfortran rpm which is based on gcc 4.4.0. Would
that help you?

Tony Schreiner
Boston College

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Old 02-03-2010, 06:12 PM
Jon Forrest
 
Default Updating gfortran in CentOS 5.4?

On 2/3/2010 10:49 AM, Tony Schreiner wrote:
>

> There is also a gcc44-gfortran rpm which is based on gcc 4.4.0. Would
> that help you?

I wonder if that rpm allows the version of
gfortran and associated libraries it installs
to be located in something other than the default
location. This is important because I don't
want to remove the standard version of
gfortran in case something goes wrong.

(I know that the rpm command can do this
but some rpms don't allow it).

Thanks for the suggestion. I'll try this.

--
Jon Forrest
Research Computing Support
College of Chemistry
173 Tan Hall
University of California Berkeley
Berkeley, CA
94720-1460
510-643-1032
jlforrest@berkeley.edu

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Old 02-03-2010, 06:14 PM
Jon Forrest
 
Default Updating gfortran in CentOS 5.4?

On 2/3/2010 10:03 AM, Akemi Yagi wrote:

>
> Regarding the compilation question, you may want to try the CHARMM forums at:
>
> http://www.charmm.org/ubbthreads/ubbthreads.php?ubb=cfrm

That's a good idea. I wasn't going to do this
because my problem really isn't a charmm problem
but you're right, other charmm users might have
faced this too.

Jon

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Old 02-04-2010, 07:51 AM
Laurent Wandrebeck
 
Default Updating gfortran in CentOS 5.4?

2010/2/3 Jon Forrest <jlforrest@berkeley.edu>:
> On 2/3/2010 10:49 AM, Tony Schreiner wrote:
>>
>
>> There is also a gcc44-gfortran rpm which is based on gcc 4.4.0. Would
>> that help you?
>
> I wonder if that rpm allows the version of
> gfortran and associated libraries it installs
> to be located in something other than the default
> location. This is important because I don't
> want to remove the standard version of
> gfortran in case something goes wrong.
>
> (I know that the rpm command can do this
> but some rpms don't allow it).
>
> Thanks for the suggestion. I'll try this.
gcc44 and gfortran44 are specially crafted to be installed without
removing official version of gcc/gfortran.
executables names are gcc44 and gfortran44.
HTH,
Laurent
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