Dear Bertrand,
Did tleap successfully compile? Or did you get any strange error messages at
the end of the build. For example one situation I could envisage is that
your $AMBERHOME/exe/ directory wasn't clean when you started and actually
contained executables built for some other system - say and Intel Pentium 4.
Then when you built the source code the leap installation (which is the last
thing to be done) failed and so you got left with the P4 executable in the
exe directory. This would almost certainly give you a problem.
Problems that typically occur with leap compilation is the X11 development
libraries not being installed on the machine but this should affect xLeap,
not tleap.
This one will be a little difficult to debug what is going on. The most
useful thing would be to see a copy of $AMBERHOME/src/config.h and a
complete copy of the build log.
For example, do the following.
cd $AMBERHOME/exe/
rm -f *
cd ../src/
make clean
./configure -nopar sgi_altix
"edit config.h and change FFLAGS from -O2 to -O0" - DO NOT CHANGE FOPTFLAGS
make >& make.log
send me config.h and make.log.
Can you also send me the output from:
ifort -V
icc -V
uname -a
For reference on the SGI Altix I have access to these versions are:
[~/amber9]$ ifort -V
Intel(R) Fortran Itanium(R) Compiler for Itanium(R)-based applications
Version 8.1 Build 20050311 Package ID: l_fc_pc_8.1.025
Copyright (C) 1985-2005 Intel Corporation. All rights reserved.
FOR NON-COMMERCIAL USE ONLY
[~/amber9]$ icc -V
Intel(R) C++ Itanium(R) Compiler for Itanium(R)-based applications
Version 8.1 Build 20041021 Package ID: l_cc_pu_8.1.024
Copyright (C) 1985-2004 Intel Corporation. All rights reserved.
FOR NON-COMMERCIAL USE ONLY
[~/amber9]$ uname -a
Linux 2.4.21-sgi240r1 #1 SMP Sat Jan 24 01:11:52 PST 2004 ia64 unknown
If I use the following installation procedure for a CLEAN directory and the
amber9.tgz file from the original cd:
1) edit ~/.cshrc and add:
source /opt/intel_fc_80/bin/ifortvars.csh
source /opt/intel_cc_80/bin/iccvars.csh
setenv AMBERHOME ~/amber9_release/amber9/
Then logout and login:
>which ifort
/opt/intel_fc_80/bin/ifort
>which icc
/opt/intel_cc_80/bin/icc
2) mkdir ~/amber9_release
3) cp /mnt/cdrom/amber9.tgz ~/amber9_release/
4) cd ~/amber9_release/
5) tar xvzf amber9.tgz
6) cd amber9
7) wget
http://amber.scripps.edu/bugfixes/9.0/bugfix.all
8) patch -p0 -N -r patch_rejects < bugfix.all
(All patches successfully, no rejects)
9) cd src/
10) ./configure -nopar sgi_altix
AMBERHOME is set to /usr/people/xxx/amber9_release/amber9
Setting up Amber configuration file for architecture: sgi_altix
Using parallel communications library: none
Using LAPACK and BLAS from SCSL.
The configuration file, config.h, was successfully created.
11) Edit $AMBERHOME/src/sander/pb_force.f (remove first line
compile=optimized)
12) cd $AMBERHOME/src/sander/
13) rm -f depend
14) ./makedepend > depend
15) cd ..
16) make
This completes with only warnings (no errors) and ends with:
Finished with the install of LEaP
make[1]: Leaving directory `/usr/people/xxx/amber9_release/amber9/src/leap'
Installation of Amber9 (serial) is complete at Thu Mar 29 09:18:29 PST 2007.
14) cd ../test
15) make
TEST_FAILURES.diff consists of innocuous differences with:
jar
crambin_md_calc_mulliken
mdout.notimaged_md_pme_qmewald_lowmem
amoeba_jac.mdout
ash.mol2
fluorescein.mol2
DGN.mol2
total.prepi
Then from this I can then build a parallel version as follows:
1) cd $AMBERHOME/src
2) make clean
3) ./configure -mpi sgi_altix
4) make paralllel
5) setenv DO_PARALLEL 'mpirun -np 2'
6) cd ../test
7) make test.parallel
You should then also compile PMEMD for sgi_altix in parallel as well as this
gives the best parallel performance.
All the best
Ross
/\
\/
|\oss Walker
| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk <
http://www.rosswalker.co.uk/> | PGP Key
available on request |
Note: Electronic Mail is not secure, has no guarantee of delivery, may not
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_____
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
bertrand russell
Sent: Thursday, March 29, 2007 02:04
To: amber.scripps.edu
Subject: Re: AMBER: SGI Altix Compilation Problems (Was: Error - must define
AMBERHOME environment variable)
Dear Mr. Ross,
I tried to compile with "O0" instead of "O3". My
compilation went successful but I am getting the following error while
testing,
###################################################
==============================================================
ptraj: test ptraj on averaging les trajectory to normal trajectory
diffing hef_averaged.crd.save with hef_averaged.crd
PASSED
==============================================================
cd leap; ./Run.tleap
Running leap tests on ./tleap -> ../../exe/teLeap
building force field libraries:
'91 ff..
./Run.tleap: Program error in leap
make: *** [test.leap ] Error 1
bash-2.05b$
#################################################
What would be the problem?
--
Live Life; Don't pass it
Bertrand.P.S.Russell
+91-9894398441
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Received on Sun Apr 01 2007 - 06:07:31 PDT
