On Tue, Jun 4, 2013 at 5:48 PM, Mark Abraham wrote:
>
>
>
> On Tue, Jun 4, 2013 at 4:50 PM, Jianguo Li wrote:
>
>>
>>
>> Thank you, Mark and Xavier.
>>
>> The thing is that the cluster manager set the
>> minimum number of cores of each jobs in Bluegene/Q is 128, so I can not
>> use 64 cores. But
On Tue, Jun 4, 2013 at 4:50 PM, Jianguo Li wrote:
>
>
> Thank you, Mark and Xavier.
>
> The thing is that the cluster manager set the
> minimum number of cores of each jobs in Bluegene/Q is 128, so I can not
> use 64 cores. But according to the performance, 512 cores in Bluegene
> roughly equival
e a optimized number for --ntasks-per-node?
Cheers
Jianguo
From: Mark Abraham
To: Discussion list for GROMACS users
Cc: Jianguo Li
Sent: Tuesday, 4 June 2013, 22:32
Subject: Re: [gmx-users] Performance of Gromacs-4.6.1 on BlueGene/Q
On Tue, Jun 4, 2
on list for GROMACS users
Cc:
Sent: Tuesday, 4 June 2013, 22:20
Subject: Re: [gmx-users] Performance of Gromacs-4.6.1 on BlueGene/Q
BG CPUs are generally much slower (clock whose) but scale better.
You should try to run on 64 CPUs on the Blue gene too for faire comparison.
The number of CPUs per n
On Tue, Jun 4, 2013 at 4:20 PM, XAvier Periole wrote:
>
> BG CPUs are generally much slower (clock whose) but scale better.
>
> You should try to run on 64 CPUs on the Blue gene too for faire comparison.
> The number of CPUs per nodes is also an important factor: the more CPUs
> per nodes the mor
BG CPUs are generally much slower (clock whose) but scale better.
You should try to run on 64 CPUs on the Blue gene too for faire comparison.
The number of CPUs per nodes is also an important factor: the more CPUs per
nodes the more communications needs to be done. I observed a significant slow
Dear All,
Has anyone has Gromacs benchmark on Bluegene/Q?
I recently installed gromacs-461 on BG/Q using the following command:
cmake .. -DCMAKE_TOOLCHAIN_FILE=BlueGeneQ-static-XL-C \
-DGMX_BUILD_OWN_FFTW=ON \
-DBUILD_SHARED_LIBS=OFF \
-DGMX_XML=OFF \
-DCMAKE
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