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
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Received on Wed Oct 17 2007 - 06:07:40 PDT
