AMBER Archive (2004)

Subject: Re: AMBER: pmemd.

From: Robert Duke (rduke_at_email.unc.edu)
Date: Mon Aug 16 2004 - 09:33:21 CDT

Osman -
There are at least two things going on here:
1) You are using an intel fortran version 7 configure script with intel
fortran 8. This is understandable, since I did not release an intel fortran
8 script with amber 8 - the ifort 8 compiler did not work in the timeframe
of the amber 8 release for pmemd on ia32. Please find embedded below a
couple of config.h files that SHOULD work with ifort 8 if you plug in the
right value for the location of mpich.
2) The specific release of the intel fortran compiler, version 8, is
probably bad (the internal error listed below leads to this conclusion).
Prior to compiler release 8.0.046, intel apparently had problems allocating
space for long module names, or some other such nonsense. Be sure you have
downloaded version 8.0.046 from the intel site; later versions may or may
not also work - the intel version 8 compiler, while producing faster code,
has not been particularly stable (ie., the intel developers seem to
introduce new bugs when they take out the old ones).
3) A possible third thing going on is that stacksize should be set to
unlimited in your .login file, definitely for running pmemd, and it is
probably not a bad idea to do this when using the compiler also (but I think
your real problem is 2) above). This is done by placing a line
'limit stacksize unlimited' in your .login file if you use the csh or tcsh.
For bash, I think you would want to put 'ulimit -s unlimited' in
.bash_profile, but I don't use bash so I have not checked it out.

Here are the config.h samples:

Try using this as config.h for uniprocessor

Begin -->
#!/bin/csh -f
setenv PREPROCFLAGS
setenv CPP "/lib/cpp -traditional "
setenv OPT_LO "ifort -c -auto -tpp6 -mp1 -O0 "
setenv OPT_MED "ifort -c -auto -tpp6 -mp1 -O2 "
setenv OPT_HI "ifort -c -auto -tpp6 -mp1 -ip -O3 "
setenv LOAD "ifort"
setenv LOADLIB
<-- End

Or this for mpich:
Begin -->
#!/bin/csh -f
setenv MPICH_HOME <whereever your mpich installation is>
setenv MPICH_INCLUDE $MPICH_HOME/include
setenv MPICH_LIBDIR $MPICH_HOME/lib
setenv MPILIB "-L$MPICH_LIBDIR -lmpich"
setenv PREPROCFLAGS "-DMPI -DSLOW_NONBLOCKING_MPI"
setenv CPP "/lib/cpp -traditional -I$MPICH_INCLUDE"
setenv OPT_LO "ifort -c -auto -tpp6 -mp1 -O0"
setenv OPT_MED "ifort -c -auto -tpp6 -mp1 -O2"
setenv OPT_HI "ifort -c -auto -tpp6 -mp1 -ip -O3"
setenv LOAD "ifort"
setenv LOADLIB "$MPILIB"
<-- End

Other possible issues:

Be sure that mpich has been built with the same fortran compiler as you use
to compile pmemd. This is a recurring headache with using mpich; the
library interface names have to match the conventions used by the compiler.

The fortran compiler libraries will have to be accessible for dynamic
loading from all machines in a cluster. In an ideal world, we could
statically link all this stuff without problems. In the real world, the
static threads library that gets linked in if you link static causes
segmentation violations (a vague, but hopefully correct, recollection).

If you are using mpich over gigabit ethernet, you will want to increase the
tcp/ip buffer sizes. I have not done a rigorous study of what a good size
is, but I will check this out later today and post a separate message to the
list (this is something I have been intending to do, and not getting around
to doing). This is not an issue if you are just using a dual processor
pentium and the mpich shared memory device.

Regards - Bob

----- Original Message -----
From: "Osman Gani" <osman.gani_at_fagmed.uit.no>
To: <amber_at_scripps.edu>
Sent: Monday, August 16, 2004 9:03 AM
Subject: RE: AMBER: pmemd.

> Dear Bob,
> Following is my administrator's message pasted-
>
> Here is the messages I receive from my machine(Redhat Linux 8,0 on Dell
Xeon 2,8 G preocessor) when trying to install pmemd:
>
> ./configure linux_p4 ifc7 mpich
> Please enter name of directory where MPICH files are installed:
> /usr/local/mpich-1.2.5
> PMEMD Configurate successfully completed.
>
> make install
> cd src; make install
> make[1]: Entering directory `/usr/local/amber8/src/pmemd/src'
> ../Compile OPT_HI -P ew_direct_cit_dat.f90
> cat ew_direct_cit_dat.f90 |
lib/cpp -traditional -I/usr/local/mpich-1.2.5/include -P -DMPI -DSLOW_NON
BLOCKING_MPI -DDIRFRC_VECT_OPT > _ew_direct_cit_dat_.f90
> ifc -c -auto -tpp7 -xW -mp1 -ip -O3 _ew_direct_cit_dat_.f90
> ifc: warning: The Intel Fortran driver is now named ifort. You can
suppress
> this message with '-quiet'
> fortcom: Severe: _ew_direct_cit_dat_.f90, line 82: **Internal compiler
error: segmentation violation signal raised** Please report this error along
with the circumstances in which it occurred in a Software Problem Report.
Note: File and line given may not be explicit cause of this error.
> contains
> ^
> compilation aborted for _ew_direct_cit_dat_.f90 (code 3)
> make[1]: *** [ew_direct_cit_dat.o] Error 1
> make[1]: Leaving directory `/usr/local/amber8/src/pmemd/src'
> make: *** [install] Error 2
>
> And here is teh result when compiling without mpich:
>
>
> [root_at_mia pmemd]# ./configure linux_p4 ifc7 nopar
> PMEMD Configurate successfully completed.
>
> [root_at_mia pmemd]# make install
> cd src; make install
> make[1]: Entering directory `/usr/local/amber8/src/pmemd/src'
> ../Compile OPT_HI -P ew_direct_cit_dat.f90
> cat ew_direct_cit_dat.f90 | /lib/cpp -traditional -P -DDIRFRC_VECT_OPT
> _ew_direct_cit_dat_.f90
> ifc -c -auto -tpp7 -xW -mp1 -ip -O3 _ew_direct_cit_dat_.f90
> ifc: warning: The Intel Fortran driver is now named ifort. You can
suppress this message with '-quiet'
> fortcom: Severe: _ew_direct_cit_dat_.f90, line 80: **Internal compiler
error: segmentation violation signal raised** Please report this error along
with the circumstances in which it occurred in a Software Problem Report.
Note: File and line given may not be explicit cause of this error.
> contains
> ^
> compilation aborted for _ew_direct_cit_dat_.f90 (code 3)
> make[1]: *** [ew_direct_cit_dat.o] Error 1
> make[1]: Leaving directory `/usr/local/amber8/src/pmemd/src'
> make: *** [install] Error 2
>
> I am not sure what are the error messages indicate. I am enthusiastic to
work with pmemd.
>
> Regards,
> Osman
>
> -----Original Message-----
> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu]On Behalf
> Of Robert Duke
> Sent: 23. juli 2004 19:47
> To: amber_at_scripps.edu
> Subject: Re: AMBER: pmemd.
>
>
> Osman -
> Two issues:
> 1) pmemd is basically a fast version of sander, that does a subset of the
> total sander functionality. The command line to use is the same as
sander,
> and is thus documented in the sander section of the manual. The pmemd
> section of the manual is more involved in specifying the differences
between
> pmemd and sander, if I remember correctly.
> 2) pmemd is built in a separate step from the rest of amber in amber 8.
> This is a consequence mostly of pmemd being available for a different set
of
> platforms and optimizing a bit differently. Dave Case would have liked to
> unify the build (and rightly so), but I was more concerned about messing
> things up. SO to have pmemd available, you have to go to the
> amber8/src/pmemd directory, read the README, invoke the configure script
> that is there with arguments (given if you do a ./configure -help), and
then
> do a 'make install' in the pmemd directory (you will also need to do a
> 'rehash' afterward for the csh to pick up the new executable, and have
> $AMBERHOME/exe in your path (hardwired, or with $AMBERHOME defined prior
to
> PATH def)). There is a little installation info in the amber 8 manual
> (pmemd section), and more info in the amber8/src/pmemd/README file (some
of
> this is more than you need to know unless you are porting pmemd to a
> currently unsupported platform).
> Regards - Bob Duke
>
> ----- Original Message -----
> From: "Osman Gani" <osman.gani_at_fagmed.uit.no>
> To: <amber_at_scripps.edu>
> Sent: Friday, July 23, 2004 1:09 PM
> Subject: AMBER: pmemd.
>
>
> > I want to run pmemd in AMBER8 on Redhat Linux.I don't see any command
line
> usage for that in the manual.When I invoke "pmemd" it doesn't get the
> command.What could be the problem?May be I am asking a naive question.But
I
> have to do hurry to go.
> > Thanks in advance.
> >
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