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