from:"Bernhard Bandow"

Re: [gmx-users] problems with gmxtest.pl

2009-03-13 Thread Bernhard Bandow

Dear users and developers,

the tests were run on one node of a linux cluster employing 8 cores.
Each node is a dual socket blade with two quad core cpus.
/proc/cpuinfo says:

processor   : 0
vendor_id   : GenuineIntel
cpu family  : 6
model   : 23
model name  : Intel(R) Xeon(R) CPU   E5472  @ 3.00GHz
stepping: 6
cpu MHz : 2992.496
cache size  : 6144 KB
physical id : 0
siblings: 4
core id : 0
cpu cores   : 4
fpu : yes
fpu_exception   : yes
cpuid level : 10
wp  : yes
flags   : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge
mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm syscall
nx lm constant_tsc pni monitor ds_cpl vmx est tm2 cx16 xtpr dca lahf_lm
bogomips: 5990.08
clflush size: 64
cache_alignment : 64
address sizes   : 38 bits physical, 48 bits virtual
power management:

... until processor 7

The OS is SUSE Linux Enterprise Server 10 (x86_64), version 10,
patchlevel 2.
Gromacs was build on this system as I have posted before.

Best regards

Bernhard Bandow

David van der Spoel schrieb:
 bandow wrote:
 Dear users and developers of gromacs,

 despite checking for the usage of the proper version of tests after
 upgrading to gromacs-4.0.4 the test suite still produces results with
 the status FAILED. This is the case for some tests in kernel, complex,
 and pdb2gmx.
 For example kernel020 fails with
 
 So how is this done? Hardware, OS, #cpus?
 
 /kernel020/checkvir.out  containing:

 LJ-14step   0:  -63.1209,  step   0:  6.50743
 Potentialstep   0:  -321.601,  step   0: -251.973
 Kinetic En.  step   0:   15.0135,  step   0:  29.0739
 Total Energy step   0:  -306.588,  step   0: -222.899
 Temperature  step   0:   1.93226,  step   0:  3.74185
 Pressure (bar)   step   0:  -3095.37,  step   0:  -2497.8
 Vir-XX   step   0:   1127.45,  step   0:  1075.85
 Vir-XY   step   0:63.524,  step   0:  21.7767
 Vir-XZ   step   0:  -264.813,  step   0: -260.354
 Vir-YX   step   0:   63.5241,  step   0:  21.7771
 Vir-YY   step   0:   803.252,  step   0:  581.703
 Vir-ZX   step   0:  -264.813,  step   0: -260.355
 Vir-ZZ   step   0:   321.207,  step   0:  176.573

 Any hints to locate the reasons for this behavior are appreciated.

 Best regards

 Bernhard Bandow

 -- 
 -
   Dr. Bernhard BandowPhone: +49 511  762 794727
   Leibniz Universitaet Hannover  FAX:   +49 511  762 3003
   RRZN / HLRNEmail: ban...@rrzn.uni-hannover.de
   Schlosswender Str. 5
   D-30159 Hannover   http://www.rrzn.uni-hannover.de/
   Germanyhttp://www.hlrn.de/
 -

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[gmx-users] problems with gmxtest.pl

2009-03-12 Thread Bernhard Bandow

Dear users and developers of gromacs,

although running the tests is straight forward some advice how to
interpret the results would be helpful.
If a test ends with
Testing xyz . . . PASSED but check mdp file differences
and 'diff' of the mdp files shows a differenet file header only
everything seems to be fine. Is this right?

One of the 45 pdb2gmx tests fails. Presumably it is that one which puts
its files into:
pdb2gmx/pdb-6pti/ffencads/none/spc
The potential energies of the other tests in ener.log deviate from those
in reference_s.log. Is there a rule of thumb how small the deviations
should be in order to be tolerable?

Best regards

Bernhard Bandow

--
-
  Dr. Bernhard BandowPhone: +49 511  762 794727
  Leibniz Universitaet Hannover  FAX:   +49 511  762 3003
  RRZN / HLRNEmail: ban...@rrzn.uni-hannover.de
  Schlosswender Str. 5
  D-30159 Hannover   http://www.rrzn.uni-hannover.de/
  Germanyhttp://www.hlrn.de/
-

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[gmx-users] problems with gmxtest.pl

2009-03-11 Thread Bernhard Bandow

Dear users and developers of gromacs,

following the installation of gromacs 4.0.3 the tests show some
inconsistencies.
The software was compiled with Intel 11.0.069 compiler using mvapich2
Further options in configure were:
--enable-fortran
--enable-mpi
--with-fft=mkl
--enable-shared
The system gromacs is intended to run on uses mpiexec to initiate
message passing. So gmxtest.pl was modified at line 31 to:

  $mdprefix = mpiexec -np $parallel

The output in mdrun.out starts with

  -- NNODES=4, MYRANK=2, HOSTNAME=h01001
  NNODES=4, MYRANK=0, HOSTNAME=h01001
  NODEID=0 argc=1
  NNODES=4, MYRANK=1, HOSTNAME=h01001
  NODEID=1 argc=1
  NNODES=4, MYRANK=3, HOSTNAME=h01001
  NODEID=3 argc=1
  NODEID=2 argc=1
   :-)  G  R  O  M  A  C  S  (-:

...it seems to be a parallel run indeed.
Nontheless grompp.out of the corresponding run contains the lines:

---
Program grompp, VERSION 4.0.3
Source code file: statutil.c, line: 727

Invalid command line argument:
-np
---

which is related to line 159 of gmxtest.pl.

Are there any comments to the usage and position of the -np argument
under these circumstances in order to have more than an educated guess
for that?

Best regards

Bernhard Bandow

--
-
  Dr. Bernhard BandowPhone: +49 511  762 794727
  Leibniz Universitaet Hannover  FAX:   +49 511  762 3003
  RRZN / HLRNEmail: ban...@rrzn.uni-hannover.de
  Schlosswender Str. 5
  D-30159 Hannover   http://www.rrzn.uni-hannover.de/
  Germanyhttp://www.hlrn.de/
-
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Re: [gmx-users] problems with gmxtest.pl

[gmx-users] problems with gmxtest.pl

[gmx-users] problems with gmxtest.pl

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