[gmx-users] Problem configuring openMPI

[Manik Mayur]

On Wed, Mar 4, 2009 at 2:25 AM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> Manik Mayur wrote:
>
>>
>>
>> On Wed, Mar 4, 2009 at 1:55 AM, Roland Schulz <roland at utk.edu <mailto:
>> roland at utk.edu>> wrote:
>>
>>    You will have to recompile everything:
>>    make clean
>>    make
>>
>>
>> I tried that but to no avail, then I tried building static libs by
>> removing --enable-shared in ./configure and it got compiled and installed
>> properly.
>> Thanks to all, as for now, its working to my need.
>> But somehow still I feel that with openmpi-1.3, gromacs-4.0.4 and Xeon
>> Quad core at 3.6Ghz, the processing speed which I am getting, is quite low.
>>
>
> This comment won't help you fix the issue. You need to start by telling us
> why you think the speed is low, and under what conditions you are testing.
> If you aren't using an optimized FFT package you will get slow throughput
> with PME.


Yes, I do need to run some more tests before commenting on the speed issue.
However, I just found that the processor is not Xeon Quad core @ 3.6 Ghz.
The output of $cat /proc/cpuinfo is:

-bash-2.05b$ cat /proc/cpuinfo
processor    : 0
vendor_id    : GenuineIntel
cpu family    : 15
model        : 4
model name    : Intel(R) Xeon(TM) CPU 3.60GHz
stepping    : 1
cpu MHz        : 3600.248
cache size    : 1024 KB
physical id    : 0
siblings    : 2
runqueue    : 0
fdiv_bug    : no
hlt_bug        : no
f00f_bug    : no
coma_bug    : no
fpu        : yes
fpu_exception    : yes
cpuid level    : 5
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 nx lm
bogomips    : 7182.74

processor    : 1
vendor_id    : GenuineIntel
cpu family    : 15
model        : 4
model name    : Intel(R) Xeon(TM) CPU 3.60GHz
stepping    : 1
cpu MHz        : 3600.248
cache size    : 1024 KB
physical id    : 3
siblings    : 2
runqueue    : 1
fdiv_bug    : no
hlt_bug        : no
f00f_bug    : no
coma_bug    : no
fpu        : yes
fpu_exception    : yes
cpuid level    : 5
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 nx lm
bogomips    : 7182.74

processor    : 2
vendor_id    : GenuineIntel
cpu family    : 15
model        : 4
model name    : Intel(R) Xeon(TM) CPU 3.60GHz
stepping    : 1
cpu MHz        : 3600.248
cache size    : 1024 KB
physical id    : 0
siblings    : 2
runqueue    : 0
fdiv_bug    : no
hlt_bug        : no
f00f_bug    : no
coma_bug    : no
fpu        : yes
fpu_exception    : yes
cpuid level    : 5
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 nx lm
bogomips    : 7182.74

processor    : 3
vendor_id    : GenuineIntel
cpu family    : 15
model        : 4
model name    : Intel(R) Xeon(TM) CPU 3.60GHz
stepping    : 1
cpu MHz        : 3600.248
cache size    : 1024 KB
physical id    : 3
siblings    : 2
runqueue    : 1
fdiv_bug    : no
hlt_bug        : no
f00f_bug    : no
coma_bug    : no
fpu        : yes
fpu_exception    : yes
cpuid level    : 5
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 nx lm
bogomips    : 7182.74

Mark
>
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-- 
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
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