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,
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
On 2/3/2010 10:03 AM, Akemi Yagi wrote:
Regarding the compilation question, you may want to try the CHARMM forums at:
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
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
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.
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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Akemi Yagi -
Jon Forrest -
Laurent Wandrebeck -
Tony Schreiner