on that machine, I suspect you have an outdated
compiler. What compiler are you using?
2014-08-27 12:00 GMT+02:00 Szilárd Páll pall.szil...@gmail.com:
Normally the highest supported SIMD instructions set, which is in your
case AVX2, is detected during configuration phase. The fact that you
certainly outperform icc.
Cheers,
--
Szilárd
It only works with 12.1 unless a header of CUDA 5.5 to be modified.
Theo
On 8/25/2014 9:44 PM, Szilárd Páll wrote:
On Mon, Aug 25, 2014 at 8:08 AM, Mark Abraham mark.j.abra...@gmail.com
wrote:
On Mon, Aug 25, 2014 at 5:01 AM, Theodore Si sjyz
On Mon, Aug 25, 2014 at 8:08 AM, Mark Abraham mark.j.abra...@gmail.com wrote:
On Mon, Aug 25, 2014 at 5:01 AM, Theodore Si sjyz...@gmail.com wrote:
Hi,
https://onedrive.live.com/redir?resid=990FCE59E48164A4!
2572authkey=!AP82sTNxS6MHgUkithint=file%2clog
On Mon, Aug 25, 2014 at 7:12 PM, Xingcheng Lin
linxingcheng50...@gmail.com wrote:
Theodore Si sjyzhxw@... writes:
Hi,
https://onedrive.live.com/redir?
resid=990FCE59E48164A4!2572authkey=!AP82sTNxS6MHgUkithint=file%2clog
https://onedrive.live.com/redir?
On Thu, Aug 21, 2014 at 8:25 PM, Yunlong Liu yliu...@jh.edu wrote:
Hi Roland,
I just compiled the latest gromacs-5.0 version released on Jun 29th. I will
recompile it as you suggested by using those Flags. It seems like the high
loading imbalance doesn't affect the performance as well, which
Hi,
No need to worry, GTX 680 is quite recent and will be supported by
GROMACS for at least a couple of years longer. Just make sure this
second hand GPU is i) stable (run cuda-memtest) ii) is sold cheaper
than a GTX 770 (which is faster).
Cheers,
--
Szilárd
On Mon, Aug 18, 2014 at 4:34 PM,
On Tue, Aug 19, 2014 at 4:19 PM, Theodore Si sjyz...@gmail.com wrote:
Hi,
How can we designate which CPU-only nodes to be PME-dedicated nodes?
mpirun -np N mdrun_mpi -npme M
Starts N ranks out of which M will be PME-only and (M-N) PP ranks.
What
mdrun options or what configuration should
13% is not that large and as far as I can tell the dynamic load
balancing has not even kicked in (the above message would show the
min/average cell volume due to the domain rescaling).
You can try manually turning on load balancing with -dlb yes.
--
Szilárd
On Mon, Aug 18, 2014 at 7:14 PM,
-decomposition for the next version.
I have
plans to overclock the CPUs by 10-20%.
That should work quite well.
--
Szilárd
On Tuesday, 12 August 2014 9:11 PM, Szilárd Páll pall.szil...@gmail.com
wrote:
Yes, it definitely will. The difference will be quite pronounced in
CPU-only runs
You do not show your exact hardware configuration and with different
CPUs you will surely get different performance. You do not show your
command line or launch configuration (#ranks, #threads, #separate PME
ranks) either, but based on the -gpu_id argument you have
there, I assume you are
borderline
useless, but with the RDMA protocol iWARP over 10 and 40 GB Ethernet,
I've seen people report decent results.
Regards,
Abhishek
On Tue, Aug 5, 2014 at 5:46 PM, Szilárd Páll pall.szil...@gmail.com wrote:
Hi,
You need fast network to parallelize across multiple nodes. 1 Gb
ethernet
Hi,
You need fast network to parallelize across multiple nodes. 1 Gb
ethernet won't work well and even even 10/40 Gb ethernet needs to be
of good quality; you'd likely need to buy separate adapters, the
on-board ones won't perform well. I posted some links to the list
related to this a fed days
?
From: Szilárd Páll pall.szil...@gmail.com
To: Michael Brunsteiner mbx0...@yahoo.com
Sent: Thursday, July 17, 2014 2:00 AM
Subject: Re: [gmx-users] hardware setup for gmx
Dear Michael,
I'd appreciate if you kept the further discussion on the gmx-users list
On Thu, Jul 31, 2014 at 12:35 AM, Szilárd Páll pall.szil...@gmail.com wrote:
Dear Michael,
On Wed, Jul 30, 2014 at 1:49 PM, Michael Brunsteiner mbx0...@yahoo.com
wrote:
Dear Szilard,
sorry for bothering you again ... regarding performance tuning by adjusting
the VdW and Coulomb cut-offs
On Mon, Jul 28, 2014 at 6:48 AM, Theodore Si sjyz...@gmail.com wrote:
Hi all,
In the log file, what do count, wall t(s) G-Cycles mean? It seems that
the last column is the percentage of G-Cycles.
Wall t (s) = wall-clock time spent in the respective part of code
G-cycles = total giga- CPU
On Fri, Jul 25, 2014 at 12:33 PM, Mark Abraham mark.j.abra...@gmail.com wrote:
On Fri, Jul 25, 2014 at 1:51 AM, Szilárd Páll pall.szil...@gmail.com
wrote:
Hi
In general, virtualization will always have an overhead, but if done
well, the performance should be close to that of bare metal
Hi,
There is a certain version of MPI that caused a lot of headache until
we realized that it is buggy. I'm not entirely sure what version was
it, but I suspect it was the 1.4.3 shipped as default on Ubuntu 12.04
server.
I suggest that you try:
- using a different MPI version;
- using a single
On Fri, Jul 25, 2014 at 12:48 AM, Sikandar Mashayak
symasha...@gmail.com wrote:
Thanks Mark. -noconfout option helps.
For benchmarking purposes, additionally to -noconfout I suggest also using:
* -resethway or -resetstep: to exclude initialization and
load-balancing at the beginning of the run
On Fri, Jul 25, 2014 at 1:51 AM, Szilárd Páll pall.szil...@gmail.com wrote:
Hi
In general, virtualization will always have an overhead, but if done
well, the performance should be close to that of bare metal. However,
for GROMACS the ideal scenario is exclusive host access (including
Hi
In general, virtualization will always have an overhead, but if done
well, the performance should be close to that of bare metal. However,
for GROMACS the ideal scenario is exclusive host access (including
hypervisor) and thread affinities which will both depend on the
hypervisor
On Wed, Jul 23, 2014 at 12:32 AM, Sikandar Mashayak
symasha...@gmail.com wrote:
Hi,
I am checking out GPU performance of Gromacs5.0 on a single node of a
cluster.
The node has two 8-core Sandy Bridge Xeon E5-2670 and two NVIDIA K20x GPUs.
My question - is there a restriction on how many
On Fri, Jul 18, 2014 at 7:31 PM, Yunlong Liu yliu...@jhmi.edu wrote:
Hi,
Thank you for your reply.
I am actually not doing anything unusual, just common MD simulation of a
protein. My system contains ~25 atoms, more or less depend on how many
water molecules I put in it.
The way I
On Fri, Jul 18, 2014 at 8:25 PM, Yunlong Liu yliu...@jhmi.edu wrote:
Hi Mark,
I post up my log file for the run here. Thank you.
Log file opened on Wed Jul 16 11:26:51 2014
Host: c442-403.stampede.tacc.utexas.edu pid: 31032 nodeid: 0 nnodes: 4
GROMACS:mdrun_mpi_gpu, VERSION 5.0-rc1
,
--
Szilárd
Yunlong
发件人: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
gromacs.org_gmx-users-boun...@maillist.sys.kth.se 代表 Szilárd Páll
pall.szil...@gmail.com
发送时间: 2014年7月19日 2:41
收件人: Discussion list for GROMACS users
主题: Re: [gmx-users] 答复
Hi,
Benchmarking and tuning is generally quite machine-specific, but you
could have a look at this great work done by Carsten Kutzner on
SuperMUC:
http://www.mpibpc.mpg.de/11832367/kutzner13talk-Parco.pdf
https://www.mpibpc.mpg.de/14613164/Kutzner_2014_ParCo-conf2013.pdf
On Thu, Jul 17, 2014 at
Hi,
I don't see anything obviously wrong with your setup; there are two
peculiarities that I suggest looking into:
- you seem to be running in a virtualized environment (at least the
hostname indicates this); check if the flags /proc/cpuinfo contains
rdtscp and if it does not try setting
). Could you explain
me what it is happened in Cut-off schemes = verlet?
And is it possible to have the trajectory with the right bonds (not broken
bond)?
Kind Regards,
On Sun, May 25, 2014 at 5:39 PM, Szilárd Páll pall.szil...@gmail.com
wrote:
On Sat, May 24, 2014 at 9:39 PM, Que Pasa
Hi,
Never seen this error, it looks like the compiler chokes on some boost
header. At the same time, the __int128-related error seems to
indicate that setting the -gcc-version=XYZ flag to some older gcc
(e.g. 4.5/4.6) and by that requesting compatibility mode with the
specified gcc version could
On Tue, Jul 15, 2014 at 5:41 PM, Mark Abraham mark.j.abra...@gmail.com wrote:
Hi,
I would not have thought that was possible,
It can happen e.g. if you configure with SSE4.1 acceleration, but you
also use e.g. the -mfma4 or -march=bdver1 compiler flag.
but the recommended solution is
to
So, Andy, could you share the log file the above command produced?
--
Szilárd
On Tue, Jul 15, 2014 at 11:22 PM, Szilárd Páll pall.szil...@gmail.com wrote:
On Tue, Jul 15, 2014 at 5:41 PM, Mark Abraham mark.j.abra...@gmail.com
wrote:
Hi,
I would not have thought that was possible,
It can
On Fri, Jul 11, 2014 at 12:18 PM, Nidhi Katyal
nidhikatyal1...@gmail.com wrote:
Hello all
I am trying to run my job on 2 nodes by utilizing all available cores. On
each node of the cluster, we have two GPUs and two sockets with 8 cores
each.
Every time I am submitting the job, we find that
On Thu, Jul 10, 2014 at 11:10 AM, Ondrej Kroutil okrou...@gmail.com wrote:
Dear Mark,
Thank for suggestion concerning switching between CPU and GPU. Second
option was the one I was looking for! Thank you.
And this reminds me I have one remark about new 5.0 version: in previous
versions, when
On Thu, Jul 3, 2014 at 4:05 PM, Michael Brunsteiner mbx0...@yahoo.com
wrote:
Hi,
I am sorry in case I overlooked the answers in the release-notes,
but I didn't find there answers to:
1) does gmx-5.0 support free energy calculations + GPU ?
Yes.
2) does gmx-5.0 support double
Hi,
Please have a look at the gmx-users history, there has been recent
discussions about this topic.
Brief answer:
* If you only/mostly run GROMACS using GPU, Intel CPUs with many fast cores
combined with high-end Geforce GTX cards will give the best performance/$;
e.g. currently i7 4930K + GTX
The link is correct, something must be broken on your side. Try using e.g. wget:
$ wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.tar.gz ls -l gromacs*.gz
--2014-07-02 22:34:44-- ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.tar.gz
= `gromacs-5.0.tar.gz'
Resolving
On Wed, Jul 2, 2014 at 11:08 PM, Justin Lemkul jalem...@vt.edu wrote:
On 7/2/14, 4:36 PM, Szilárd Páll wrote:
The link is correct, something must be broken on your side. Try using e.g.
wget:
$ wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.tar.gz ls -l
gromacs*.gz
--2014-07-02 22:34
On Fri, Jun 27, 2014 at 11:36 AM, Thomas Evangelidis teva...@gmail.com wrote:
Thank you all for your comment!
The helix dimer is not very stable and I know that from extensive
accelerated MD simulations I've done with AMBER using various boost values.
Now I want to use a different force field
an entirely different system at small
lambda factors.
--
Szilárd
On Wed, Jun 25, 2014 at 6:21 PM, Szilárd Páll pall.szil...@gmail.com wrote:
Hi,
Next time, you should perhaps use plz, ... (and other eye-catching
formatting marks); a nice mix of font colors and typefaces could also
help to highlight
Hi,
In this case you can't do much, the GPU is simply not fast enough to
finish its job before the CPU does. What you can try is:
- decrease nstlist - especially if it has been increased by mdrun
(hint use GMX_NSTLIST)
- try running in mixed GPU+CPU non-bonded mode, e.g.
mdrun -ntmpi 2 -gpu_id 00
On Sat, May 24, 2014 at 9:39 PM, Que Pasa quepas...@gmail.com wrote:
Yes. You can. The entire program was built and was functional on CPUs well
before GPUs came into the picture. Due to the way calculations are
off-loaded to GPUs not all features available on CPUs are available in the
GPU
Yes. However, a larger nstlist can be often faster with GPUs (and at
high parallelization). mdrun will by default try to increase nstlist,
but only if the value set in the mdp is quite low, IIRC 20. Hence, if
you set nstlis=20 in the mdp, you won't get the automatic switching to
25 or 40 -
http://www.gromacs.org/Documentation/Installation_Instructions#4.2._Using_CMake_command-line_options
With 4.5/6 we generate a target with CMake called install-mdrun, so
make install-mdrun
will work.
With 5.0 things will change a bit and you'll have to turn on an
mdrun-only build.
--
Szilárd
Hi,
Sounds like an MPI or MPI+CUDA issue. Does mdrun run if you use a
single GPU? How about two?
Btw, unless you have some rather exotic setup, you won't be able to
get much improvement from using more than three, at most four GPUs per
node - you need CPU cores to match them (and a large system
This just tells that two GPU-s were detected but only the first one
was automatically selected to be used - presumably because you
manually specified the number of ranks (-np or -ntmpi) to be one.
However, your mail contains neither the command line you started mdrun
with, nor (a link to) the log
Hi,
The Verlet scheme supports free energy calculation in 5.0; it works
with GPUs too, but not in double precision.
However, I suggest you consider first whether you really *need* double
precision. If you do, it may still be beneficial for you to use the
Verlet scheme in 5.0 -- especially if you
On Sat, May 10, 2014 at 10:40 PM, Albert mailmd2...@gmail.com wrote:
it is better to choose a stable Linux for computational work. I recommend
the following:
Redhat Enterprise, Scientific Linux,SuSE Linux Enterprise
Ubuntu is on not stable enough for professional work according to my own
On Wed, May 7, 2014 at 2:13 PM, Harry Mark Greenblatt
harry.greenbl...@weizmann.ac.il wrote:
BSD
So a job should run the same or faster on 10 cores at 2.5GHz relative to 6
cores at 3.5GHz?
Thanks for letting me know
Well, the guesstimation is not bulletproof, so if you want to be
also be helpful to have your latest input files that you obtained the
above results with, preferably mdp,gro, top.
Cheers,
--
Szilárd
On Mon, May 5, 2014 at 5:32 PM, Szilárd Páll pall.szil...@gmail.com wrote:
On Mon, May 5, 2014 at 10:45 AM, Mark Abraham mark.j.abra...@gmail.com
wrote
Hi,
Based on the performance data you provided, I'm afraid a GTX 770 won't
be fast enough combined with a E5-2643V2 - at least for your system.
Notice in the log output that the Wait GPU local accounts for 46% of
the runtime. This is because while the bonded + PME force compute time
takes 2.77
On Thu, Apr 17, 2014 at 8:45 PM, mirc...@sjtu.edu.cn wrote:
Hi everyone,
I am trying to do some pulling simulations by gromacs (i.e., pull a ligand
from its binding site), as the system is large I want to accelerate the
simulations by GPU. I want to confirm that, Does GPU simulation support
Hi Chris,
I've got a few questions/comments.
7) -DCMAKE_INSTALL_PREFIX=/cygdrive/c/Gromacs465 is the installation
directory -DGMX_MPI=OFF With the second installation 10) to 13) you will
replace the non-mpi mdrun.exe with one that can run on multiple cores. If you
omit this step, the
Check the version header, it contain a Precision field (e.g. mdrun -version).
--
Szilárd
On Wed, Mar 12, 2014 at 9:03 AM, Dario Corrada dario.corr...@gmail.com wrote:
How I can check if a packaged version of GROMACS (such as those available
from Fedora or Ubuntu repositories) has been
That's a normal side-effect of mdrun trying to set thread affinities
[1] on a platform which does not support this. Also, this is not an
error, mdrun should have continued to run.
Note that you would be much better off with upgrading to the latest
version, there have been many improvements,
Da: Szilárd Páll pall.szil...@gmail.com
A: Discussion list for GROMACS users gmx-us...@gromacs.org; Gloria
Saracino glos...@yahoo.it
Inviato: Venerdì 21 Febbraio 2014 1:10
Oggetto: Re: [gmx-users] hybrid CPU/GPU nodes
Hi,
Unfortunately the answer is not as simple as use 6-8 cores
Your mail reads like an FYI, what is the question?
In case if you were wondering what causes this, it could be simply a
soft error, but it's hard to tell. What GPU are you running on? If
it's in your own workstation, you could consider running a longer
stress-test on it using e.g. CUDA memtest.
wrote:
I am using GTX690.
OK, I will do some test.
thank you for helpful advices.
Albert
On 02/12/2014 01:54 PM, Szilárd Páll wrote:
Your mail reads like an FYI, what is the question?
In case if you were wondering what causes this, it could be simply a
soft error, but it's hard to tell
/
Icc details :
icc version 13.0.1 (gcc version 4.4.6 compatibility)
OpenMM is not available in environment.
On Mon, Feb 10, 2014 at 6:15 PM, Szilárd Páll pall.szil...@gmail.comwrote:
On Mon, Feb 10, 2014 at 1:27 PM, Chaitali Chandratre
chaitujo...@gmail.com
On Tue, Feb 11, 2014 at 12:11 PM, unitALX alec.zan...@gmail.com wrote:
Helllo all!
In my general situation, I have a batch of homology models that I would like
to assess for stability by molecular dynamics.
I am working with a postdoc in my lab who was extensive experience with
NAMD, but
On Mon, Feb 10, 2014 at 1:27 PM, Chaitali Chandratre
chaitujo...@gmail.com wrote:
Dear Sir,
I have question w.r.t gromacs-4.6.4 installation with GPU support.
I have installed non-GPU vesion(for 4.6.4) and it works fine.
But while compiling with gpu (-DGMX_GPU=ON
More dimensions = more complex communication pattern. See
http://pubs.acs.org/doi/abs/10.1021/ct700301q
Note that it's not *always* x-y decomposition first, mdrun will look
at the dimensions of your system too. One case where manually
switching to 3D decomposition can be beneficial is when there
Exactly. The penalty of large nstlist is large buffer (rlist), but up
to 40-50 with CPUs and up to 100 with GPUs is quite realistic.
Hint: in 4.6.x you can use GMX_NSTLIST to override the value set in
the mdp. From 5.0 there will be a command line option.
Cheers,
--
Szilárd
On Thu, Feb 6, 2014
PS: The buffer is automatically calculated based on the
verlet-buffer-drift set in the mdp file, for more details see the
appendix of http://dx.doi.org/10.1016/j.cpc.2013.06.003.
--
Szilárd
On Thu, Feb 6, 2014 at 11:04 AM, Szilárd Páll pall.szil...@gmail.com wrote:
Exactly. The penalty of large
Note that your above (CPU) runs had a far from optimal PP-PME balanc
(pme mesh/force
should be close to one).
Performance instability can be caused by a busy network (how many
nodes are you running on?) or even incorrect affinity settings.
If you post a/some log files, we may be able to tell
On Tue, Feb 4, 2014 at 2:31 AM, Mark Abraham mark.j.abra...@gmail.com wrote:
On Tue, Feb 4, 2014 at 1:51 AM, cyberjhon cyberj...@hotmail.com wrote:
Dear Szilárd
Thanks for your answer.
To submit the job I do;
qsub -l nodes=2:ppn=16,walltime=12:00:00
Then, to run gromacs I can do:
aprun
John,
I strongly suggest that you consult the Blue Waters or other XK7
manual or talk to the support team. Understanding this hardware in
crucial in getting any reasonable performance.
As I said before, the inconsistency in your commands is that you
request nnodes x nppn = 2 x 16 MPI ranks which
Note that both Opteron 2354 K10/Barcelona (http://goo.gl/6hyfO) and
the Xeon 53xx / Clovertown (http://goo.gl/6hyfO) are quite old and
none of them supports SSE4.1. Hence, pick SSE2 and build distributable
binaries (AFAIK Clovertown does not support the rdtscp instructions).
Also note that
FYI: GROMACS is known to work on IVB-E + K20 hardware, so I'm still
leaning toward thinking that this is either hardware or CUDA software
error.
On Fri, Jan 31, 2014 at 2:57 PM, AOWI (Anders Ossowicki)
a...@novozymes.com wrote:
That's just weird. The Cuda API error detected does not sound good -
That sounds strange.
Does the error happen at step? Assuming the it does occur within the
first 10 steps, here are a few things to try:
- Run cuda-memcheck mdrun -nsteps 10;
- Try running with GMX_EMULATE_GPU env. var. set? This will run the
GPU acceleration code-path, but will use CPU kernels
On Thu, Jan 30, 2014 at 2:10 PM, AOWI (Anders Ossowicki)
a...@novozymes.com wrote:
Does the error happen at step? Assuming the it does occur within the first
10 steps, here are a few things to try:
It happens immediately. As in:
$ time mdrun
snip
real0m3.312s
user0m6.768s
sys
On Thu, Jan 30, 2014 at 4:19 PM, AOWI (Anders Ossowicki)
a...@novozymes.com wrote:
Well, with a 24k system a single iteration can be done in 2-3 ms, so those
3.3 seconds are mostly initialization and some number of steps - could be
one, ten, or even hundred.
Sure, but it fails even with
On Wed, Jan 29, 2014 at 4:46 AM, Trayder Thomas
trayder.tho...@monash.edu wrote:
Curses! Kinda seemed intuitive that way. I assume the philosophy being
worked towards is that every unique run should have a unique .tpr file that
it is reproducible from?
Curiously, I ran and checked a first
Hi Anders,
This mail belongs to the users' list.
This type of error is typically a sign of the CUDA kernel failing due
to a nasty bug in the code or hardware error. The dmesg message is
suspicious and it may be a hint of hardware error (see
The behavior of most programs in case of a hardware failure is
undefined. However, as an MD simulation is quite sensitive to data
corruption, the simulation will most often crash immediately after
such an event. However, I can also imagine that mdrun ends up hanging,
e.g. waiting for data from the
On Tue, Jan 21, 2014 at 10:23 AM, Djurre de Jong-Bruinink
djurredej...@yahoo.com wrote:
Do you use this feature?
Do you use this feature with a shell other than bash?
Yes, I use this feature and missing it would be a great loss to my workflow.
However, I only use it in bash. Is the
On Wed, Jan 22, 2014 at 5:50 PM, jkrie...@mrc-lmb.cam.ac.uk wrote:
I +1 shell completions too. It would be ok for me too if they were only in
bash. I think my default shell on the cluster may be tcsh but I can change
it to bash if necessary.
I'd be happy to try helping to implement it but I
Btw, regarding symlink, I'd suggest that at least for mdrun it would
be nice to provide completion. This will also work for mdrun-only
builds.
--
Szilárd
On Wed, Jan 22, 2014 at 8:59 PM, Teemu Murtola teemu.murt...@gmail.com wrote:
Hi,
On Wed, Jan 22, 2014 at 7:40 PM,
On Tue, Jan 21, 2014 at 1:45 PM, Mark Abraham mark.j.abra...@gmail.com wrote:
Tabulated, yes. With all algorithms, who knows? Tabulated non-bondeds on
GPU, I highly doubt. GPUs are for computing, not looking up random-access
tables.
Actually, the CUDA Ewald non-bonded kernels are tabulated on
The install location is defined by CMAKE_INSTALL_PREFIX, the default
is /usr/local and you need root permission to write there. However,
you don't need to install system-wide, just install where you have
permission, e.g. your home.
On Sat, Dec 28, 2013 at 1:43 AM, Lutz Maibaum lutz.maib...@gmail.com wrote:
On Dec 24, 2013, at 2:29 AM, Szilárd Páll pall.szil...@gmail.com wrote:
Just wondering, has anybody done a comparison with the Verlet scheme?
It could be useful to know whether it produces results consistent
Just wondering, has anybody done a comparison with the Verlet scheme?
It could be useful to know whether it produces results consistent with
the 4.6 group scheme implementation or exhibits different behavior.
Cheers,
--
Szilárd
On Sun, Dec 22, 2013 at 1:08 AM, Lutz Maibaum
Hi,
That's unfortunate, but not unexpected. You are getting a 3x1x1
decomposition where the middle cell has most of the protein, hence
most of the bonded forces to calculate, while the ones on the side
have little (or none).
Currently, the only thing you can do is to try using more domains,
exactly know how to do it (and that's rather
low-level stuff anyway).
On Mon, Dec 9, 2013 at 1:02 AM, yunshi11 . yunsh...@gmail.com wrote:
Hi Szilard,
On Sun, Dec 8, 2013 at 2:48 PM, Szilárd Páll pall.szil...@gmail.com wrote:
Hi,
That's unfortunate, but not unexpected. You are getting a 3x1x1
Just to re-iterate what Henk said, this tweak is rather safe and if it
happens to cause problems, from what I've read/hear that will become
obvious quite quickly. Hence, it is worth trying - especially if you
have a CPU-GPU imbalance with your hardware and simulation system.
I have personally
Hi Henk,
Thanks for the useful comments!
When you run on a single GPU, you do get full timing details both on
CPU and GPU - just have a look at the performance tables at the end of
the log file. Alternatively you can simply run nvrpof mdrun which
will by default give you a nice overview of
On Wed, Dec 4, 2013 at 10:15 AM, João Henriques
joao.henriques.32...@gmail.com wrote:
Soon enough we will have daily releases :P
I hope you're not suggesting that we should release less frequently! :)
Mark, can you please elaborate just a tiny bit longer on how relevant were
the GPU-load
, I'll request a new install and tell them to remove the
previous version form the cluster. We don't want segmentation faults to
happen under certain circumstances :)
Thank you,
/J
On Wed, Dec 4, 2013 at 2:27 PM, Szilárd Páll pall.szil...@gmail.com wrote:
On Wed, Dec 4, 2013 at 10:15 AM
Hi,
In order to ease the maintenance of the native GPU/acceleration in
GROMACS, we are removing support for CUDA versions 3.2 and 4.0 in the
next version (5.0).
We have two options:
- Limit the change to performance impact on the GPU kernels due to the
removal of the legacy kernels, but do not
Yes, you can besides the minor command-line interface differences,
using MPI and thread-MPI works essentially the same way.
http://www.gromacs.org/Documentation/Acceleration_and_parallelization#MPI.2c.c2.a0Thread-MPI
--
Szilárd
On Thu, Nov 28, 2013 at 11:07 AM, Richa Singh
to use AMBER99SB force field with the ParmBSC0 nucleic acid
parameters, this combination can be found there.
Cheers
Tom
On 11/27/2013 02:06 PM, Szilárd Páll wrote:
Hi,
If you look at share/gromacs/top/ in the GROMACS installation
directory you can see which FF-s are included
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