AMBER Archive (2007)

Subject: AMBER: Test fails in Parallel version Amber9

From: gong wb (bnmrcamber_at_gmail.com)
Date: Tue Oct 16 2007 - 01:42:45 CDT


Hi, all,
    We have compiled serial and parallel version of Amber9. The test
of the serial version reported 4 possible errors, all of them are
round off errors. But the test of the parallel version gave other type
errors.
Our Installation Step (parallel version):
cd $AMBERHOME
cp bugfix.all ./
patch -p0 -N -r patch_rejects < ./bugfix.all
cd src
./configure -static -lam -bintraj ifort_ia32
make clean
make parallel >& make_parallel.log

We have checked the logfile and find no error message.
Here is the information about our operator system and compiler version
Operator system: Red Hat Linux 8
>uname -a
Linux nodeXX 2.4.18-26.7.xsmp #1 SMP Mon Feb 24 09:37:16 EST 2003 i686
i686 i386 GNU/Linux
Hardware:Parallel Cluster(each node have two cpus)
>cat /proc/cpuinfo
processor : 0
vendor_id : GenuineIntel
cpu family : 15
model : 2
model name : Intel(R) Xeon(TM) CPU 2.40GHz
stepping : 7
cpu MHz : 2392.217
cache size : 512 KB
Physical processor ID : 0
Number of siblings : 1
fdiv_bug : no
hlt_bug : no
f00f_bug : no
coma_bug : no
fpu : yes
fpu_exception : yes
cpuid level : 2
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
bogomips : 4750.85
(The other cpu is the same, so info omit)
Compiler version: Intel Fortran 8.1
>ifort -v
Version 8.1
>gcc -v
Reading specs from /usr/lib/gcc-lib/i386-redhat-linux/3.2/specs
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man
--infodir=/usr/share/info --enable-shared --enable-threads=posix
--disable-checking --host=i386-redhat-linux --with-system-zlib
--enable-__cxa_atexit
Thread model: posix
gcc version 3.2 20020903 (Red Hat Linux 8.0 3.2-7)

We use lam_mpi_7.1.3 for parallel calculation, it is compiled using the
same Intel C and Fortran compiler (Version 8.1)
The following is our test steps:
First, create a nodefile for lam, and the content is:
nodeXX cpu=2
nodeXX cpu=2
Then, set the DO_PARALLEL and start lamboot:
export DO_PARALLEL='/opt/lam_mpi_7.1.3/bin/mpirun -np 4'
/opt/lam_mpi_7.1.3/bin/lamboot -prefix /opt/lam_mpi_7.1.3 ./nodefile
make test.parallel >& test.log

The DIFF file is:
possible FAILURE: check rms.dif
/public/amber9/test/bintraj
1,10d0
< 1.00 0.
< 2.00 0.00998
< 3.00 0.02162
< 4.00 0.03381
< 5.00 0.04485
< 6.00 0.05458
< 7.00 0.06244
< 8.00 0.06958
< 9.00 0.07753
< 10.00 0.08657
---------------------------------------
possible FAILURE: check mdout.jar.001.dif
/public/amber9/test/jar_multi
177c177
< Etot = -3538.3785 EKtot = 478.2764 EPtot =
-4016.6548

---
>  Etot   =     -3538.3784  EKtot   =       478.2764  EPtot      =
-4016.6548
180c180
<  EELEC  =       -18.4200  EGB     =     -2503.6434  RESTRAINT  =
  3.6286
---
>  EELEC  =       -18.4199  EGB     =     -2503.6434  RESTRAINT  =
  3.6286
---------------------------------------
possible FAILURE:  check rem.log.dif
/public/amber9/test/rem_gb_4rep
26c26
<  2      1.15    234.76     -3.24    300.00    400.00      0.80
---
>  2      1.15    261.02     -4.61    300.00    400.00      0.80
---------------------------------------
possible FAILURE:  check reminfo.000.dif
/public/amber9/test/rem_gb_4rep
16,20c16,20
<  NSTEP =      100   TIME(PS) =     100.800  TEMP(K) =   234.76  PRESS
=     0.
<  Etot   =        21.0164  EKtot   =        24.2585  EPtot      =
 -3.2421
<  BOND   =        14.3725  ANGLE   =        19.8208  DIHED      =
 25.4361
<  1-4 NB =         5.7103  1-4 EEL =       182.5250  VDWAALS    =
 -5.9319
<  EELEC  =      -213.6574  EGB     =       -31.5175  RESTRAINT  =
  0.
---
>  NSTEP =      100   TIME(PS) =     100.800  TEMP(K) =   261.02  PRESS
=     0.
>  Etot   =        22.3628  EKtot   =        26.9719  EPtot      =
 -4.6092
>  BOND   =        14.9791  ANGLE   =        17.9986  DIHED      =
 25.4386
>  1-4 NB =         5.6257  1-4 EEL =       182.4183  VDWAALS    =
 -5.8981
>  EELEC  =      -213.4152  EGB     =       -31.7563  RESTRAINT  =
  0.
---------------------------------------
There are four FAILUREs, one is round off error. But we cann't figure
out the others. Hope that you can help us, thanks!

BNMRC Beijing, China 2007. 10. 16 ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber_at_scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu