Dear Walker,
I tried to test the testcase of some cases.
In the testcase in amber9, there are not difference with itanium patched and non-patched version.
In single mode, sander displayed error message in previous e-mail.
In parallel version with one process (-np 1), there are some message that is similiar with single mode but fewer than single mode.
When I executed 'make test.sander.QMMM.MPI' with 'DO_PARALLEL=mpirun -np 2', there are the following errer in crambin.out.
4. RESULTS
--------------------------------------------------------------------------------
NSTEP ENERGY RMS GMAX NAME NUMBER
1 NaN NaN 4.2278E+03 SG 373
BOND = 59.6787 ANGLE = 74.0627 DIHED = NaN
VDWAALS = 1350.9930 EEL = -2611.8056 HBOND = 0.0000
1-4 VDW = 183.5164 1-4 EEL = 1450.1218 RESTRAINT = 0.0000
PM3ESCF = -40.0704
QMMM: WARNING!
QMMM: Unable to achieve self consistency to the tolerances specified
QMMM: No convergence in SCF after 1000 steps.
QMMM: Job will continue with unconverged SCF. Warning energies
QMMM: and forces for this step will not be accurate.
QMMM: E = NaN DeltaE = NaN DeltaP = 0.0000E+00
QMMM: Smallest DeltaE = 0.1000E+31 DeltaP = 0.1000E+31 Step = 0
NSTEP ENERGY RMS GMAX NAME NUMBER
2 NaN NaN 0.0000E+00 N 1
BOND = NaN ANGLE = NaN DIHED = NaN
VDWAALS = 0.0000 EEL = 0.0000 HBOND = 0.0000
1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT = 0.0000
PM3ESCF = NaN
QMMM: WARNING!
QMMM: Unable to achieve self consistency to the tolerances specified
QMMM: No convergence in SCF after 1000 steps.
QMMM: Job will continue with unconverged SCF. Warning energies
QMMM: and forces for this step will not be accurate.
QMMM: E = NaN DeltaE = NaN DeltaP = 0.0000E+00
QMMM: Smallest DeltaE = 0.1000E+31 DeltaP = 0.1000E+31 Step = 0
Run.crambin ,Run.crambin_md and Run.crambin_md_calc_mulliken were runned with 2 process.
Run.crambin_md_qmgb2 was runned with 1 process and still run.
and
cat /proc/cpuinfo
processor : 0
vendor : GenuineIntel
arch : IA-64
family : Itanium 2
model : 1
revision : 5
archrev : 0
features : branchlong
cpu number : 0
cpu regs : 4
cpu MHz : 1595.699000
itc MHz : 1595.699000
BogoMIPS : 2390.75
processor : 1
vendor : GenuineIntel
arch : IA-64
family : Itanium 2
model : 1
revision : 5
archrev : 0
features : branchlong
cpu number : 0
cpu regs : 4
cpu MHz : 1595.699000
itc MHz : 1595.699000
BogoMIPS : 2390.75
[sunkist.alpha2 test]$ ifort -V
Intel(R) Fortran Itanium(R) Compiler for Itanium(R)-based applications
Version 9.0 Build 20051201 Package ID: l_fc_c_9.0.031
Copyright (C) 1985-2005 Intel Corporation. All rights reserved.
FOR NON-COMMERCIAL USE ONLY
If you need some files, I will post that quickly.
Thank you.
Take care
---------[ 받은 메일 내용 ]----------
제목 : AMBER: RE: I got the error meassage in testcase of QMMM
날짜 : Sat, 4 Nov 2006 10:09:13 -0800
보낸이 : "Ross Walker" <ross.rosswalker.co.uk>
받는이 : <amber.scripps.edu>
Dear Lee,
Firstly did you apply the patch I sent several days ago to address hanging
when running in parallel? Did it work?
>I installed amber9 single version in intel itanium server called white box.
>After install, I runned testcase with make test.sander.QMMM.
>In crambin_md.out, I got strange messages as follow.
This is in serial yes?
>QMMM: WARNING!
>QMMM: Unable to achieve self consistency to the tolerances specified
>QMMM: No convergence in SCF after 1000 steps.
>QMMM: Job will continue with unconverged SCF. Warning energies
>QMMM: and forces for this step will not be accurate.
>QMMM: E = -0.2405E+06 DeltaE = 0.3389E-01 DeltaP = 0.2716E-01
>QMMM: Smallest DeltaE = 0.3947E-02 DeltaP = 0.5110E-01 Step = 74
>
>vlimit exceeded for step 12; vmax = 97.6111
>
>How can I overcom this warning?
Since this test case passes on other system I have tried I once again
suspect that this is a case of the compiler not doing what it is supposed
to. Can you please give me detailed specs of the machine so that I can try
to track this down.
For this I will need:
Operating system and version
Details of "cat /proc/cpuinfo"
Compiler version (use ifort -V if the intel compiler - I need the full
version number. E.g. 9.1.033)
Options passed to ./configure
A complete copy of crambin_md.out from the above test case.
The results of "echo $TESTsander" and "echo $DO_PARALLEL" in the same shell
in which you are running make test.sander.QMMM
Is this the only test case that fails? Can you do exactly the following...
cd $AMBERHOME/test/
make clean
make
Let all tests run to completion and then send me the file
$AMBERHOME/test/TEST_FAILURES.diff
Once I have these details I can try and reproduce the problem myself and see
if I can come up with yet another workaround...
All the best
Ross
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| San Diego Supercomputer Center |
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