Re: [gmx-users] Re: GROMACS (w. OpenMPI) fails to run with -np larger than 10

On Wed, Apr 11, 2012 at 6:16 PM, Mark Abraham wrote: > On 12/04/2012 1:42 AM, haadah wrote: >> >> Could you clarify what you mean by "Sounds like an MPI configuration >> program. >> I'd get a test program running on 18 cores before worrying about anything >> else."? My problem is that i can't get

[gmx-users] Re: GPU support on GROMACS

Hi, > thought you can help with this... I'd appreciate if you kept future conversation on the mailing list. > The GROMACS website says Geforce GTX 560 Ti is supported. How about GTX 560? Yes, they are. All Fermi-class cards are supported. -- Szilárd > Thanks, > G > > -- > Gaurav Goel, PhD >

Re: [gmx-users] large scale simulation?

On a single quad 16-core Interlagos node with system size 34k atoms I get 55-60 ns/day and even with 24k atoms ~70 ns/day (solvated protein amber99 + tip3p) . On three of these nodes I think you can get close to 100 ns/day, but it will be close to the scaling limit. Have you considered vsites with

Re: [gmx-users] About the function of "-v' in mdrun

Just try and you'll see, it's not like -v is a dangerous command line option! -- Szilárd On Fri, Mar 30, 2012 at 1:10 AM, Acoot Brett wrote: > Dear All, > > There is a tutorial says the function of "-v" in mdrun is to make the md > process visible in the screen, which is correct. > > However fr

Re: [gmx-users] Vi plugin for Gromacs files

Hi Hubert, > With a coworker, we recently developed a plugin Vi to manipulate easily > Gromacs files. > It enables syntax highlighting for Gromacs files. For the moment, it works > with mdp, gro, top/itp and ndx files. > It contains also macros to comment/uncomment easily selections of a file. Th

Re: [gmx-users] 4.6 development version

The docs actually tells you: "Native GPU acceleration is supported with the verlet cut-off scheme (not with the group scheme) with PME, reaction-field, and plain cut-off electrostatics." (http://www.gromacs.org/Documentation/Parallelization_and_acceleration#GPU_acceleration) Use the cutoff-scheme

Re: [gmx-users] Scaling/performance on Gromacs 4

Hi Sara, The bad performance you are seeing is most probably caused by the combination of the new AMD "Interlagos" CPUs, compiler, operating system and it is very likely the the old Gromacs version also contributes. In practice these new CPUs don't perform as well as expected, but that is partly

Re: [gmx-users] Announcement: Large biomolecule benchmark report

I fully agree with David, it's great to have independent benchmarks! In fact, already the the previous version of the report has been of great use for us, we have referred to the results in a few occasions. -- Szilárd On Thu, Mar 15, 2012 at 2:37 PM, Hannes Loeffler wrote: > Dear all, > > we

Re: [gmx-users] Gromacs 4.5.5 GPU Error

Hi, Could you compile in Debug mode and run mdurn-gpu in gdb, it will tell more about the location and type of exception. -- Szilárd On Mon, Mar 12, 2012 at 8:47 AM, TH Chew wrote: > Hi all, > > I am trying to get the GPU version of gromacs running. I manage to install > OpenMM, compile and i

Re: [gmx-users] GROMACS stalls for NPT simulation when using -npme and -dd flags

Hi, That sounds like a memory leak. Could you please file a bug report in redmine preferably with: - configure options (+config.log or CMakeCache.txt would be ideal) - compiler version, external library versions (fft, blas, lapack) - input (tpr at least) - full mdrun command line Cheers, -- Szilá

Re: [gmx-users] Re: Gromacs-GPU benchmark test killed after exhausting the memory

Hi Efrat, It indeed looks like a memory leak. Could you please file a bug on redmine.gromacs.org? Cheers, -- Szilárd On Sun, Mar 4, 2012 at 12:21 PM, Efrat Exlrod wrote: > Hi Szilard, > > Thanks for your reply. > I used your script and I think it does look as a memory leak. Please look at >

Re: [gmx-users] Gromacs-GPU benchmark test killed after exhausting the memory

Hi, First I thought that there might be a memory leak which could have caused this if you ran for really long time. However, I've just ran the very same benchmark (dhfr with PME) for one hour, monitored the memory usage and I couldn't see any change whatsoever (see the plot attached). I've attach

Re: [gmx-users] BornSum: cudaMalloc in CUDAStream::Allocate failed out of memory

HI Adam, > I'm trying to run a mdrun-gpu simulation on a 64-bit Ubuntu system. > I'm using a 15GB GTX 580 NVIDIA GPU card with all the appropriate drivers > and cuda toolkit. > However, when I run the command: > > mdrun-gpu -s inpufile.tpr -c inputfile.gro -x outputfile.xtc -g > outputfile.log -n

Re: [gmx-users] mdrun-gpu error

19, 2012 at 8:45 PM, aiswarya pawar > wrote: >> >> Has the tesla card got to do anything with the error. Am using Nvidia >> Tesla S1070 1U server. >> >> >> On Thu, Jan 19, 2012 at 8:37 PM, Szilárd Páll >> wrote: >>> >>> And sort

Re: [gmx-users] mdrun-gpu error

yone knows what's going wrong. >> >> >> No, but you should start trying to simplify what you're doing to see where >> the problem lies. Does normal mdrun work? >> >> Mark >> >> >> Thanks >> Sent from my BlackBerry® on Reliance Mo

Re: [gmx-users] mdrun-gpu error

Hi, Most of those are just warnings, the only error I see there comes from the shell, probably an error in your script. Cheers, -- Szilárd On Wed, Jan 18, 2012 at 12:27 PM, aiswarya pawar wrote: > Hi users, > > Am running mdrun on gpu . I receive an error such as= > > WARNING: This run will g

Re: [gmx-users] tesla vs gtx

Hi, Teslas should be superior when it comes to reliability, but otherwise, for Gromacs 4.6 GeForce cards are perfectly fine and no Tesla-specific features will provide performance benefits. The only exception is GPUDirect for InfiniBand which might not work with consumer boards -- , although I don

Re: [gmx-users] Pme on gpu performance

palardo > Dept. Quimica Fisica, Univ. de Sevilla (Spain) > > On Tue, 29 Nov 2011 22:04:08 +0100, Szilárd Páll wrote: >> >> Hi Andrzej, >> >>> One more question: will a ratio of gpu/cpu units and cores be of >>> importance >>> in next gromacs releases

Re: [gmx-users] compiling with the pathscale compiler hangs on gmx_rms.c.o

Hi, I tried a Pathscale 4.0.12 nightly and except a few warnings compilation went fine. I don't have 4.0.11 around, though. However, mdrun segfaults at the very end of the run while generating the cycle and time counter table. I don't have time to look into this, but I'll get back to the issue wh

Re: [gmx-users] compiling with the PGI compiler

Hi, Pathscale seems to be as fast as gcc 4.5 on AMD Barcelona and the -march=barcelona option unfortunately doesn't seem to help much. However, I didn't try any other compiler optimization options. We do have several Magny-Cours machines around we can benchmark on, but thanks for the offer! Chee

Re: [gmx-users] compiling with the PGI compiler

On Thu, Dec 1, 2011 at 4:49 PM, Teemu Murtola wrote: > On Thu, Dec 1, 2011 at 16:46, Szilárd Páll wrote: >>> With the pgi compiler, I am most concerned about this floating point >>> overflow warning: >>> >>> ... >>> [ 19%] Building C object s

Re: [gmx-users] compiling with the PGI compiler

Hi, I've personally never heard of anybody using gromacs compiled with PGI. > I am using a new cluster of Xeons and, to get the most efficient > compilation, I have compiled gromacs-4.5.4 separately with the intel, > pathscale, and pgi compilers. I did try Pathscale a few months ago and AFAIR it

Re: [gmx-users] Pme on gpu performance

Hi Andrzej, > One more question: will a ratio of gpu/cpu units and cores be of importance > in next gromacs releases ? at the moment the code uses one core per gpu > unit, wright ? When the code is gpu parallel how can this change ? Yes, it will. We use both CPU & GPU and load balance between the

Re: [gmx-users] Pme on gpu performance

Thanks for the info. -- Szilárd On Tue, Nov 29, 2011 at 11:50 AM, Andrzej Rzepiela wrote: > Hey, > > Thank you for the info. The data that I obtained for comparison was > performed  with GTX580, 4 fs timestep and heavy hydrogen atoms instead of > constraints, as you suspected.  For dhfr with PME

Re: [gmx-users] Pme on gpu performance

allation and usage? > > Thanks a lot! > > Sincerely yours, > > Jones > > >> >> -- >> Szilárd >> >> >> >> On Sun, Nov 27, 2011 at 11:25 PM, Alexey Shvetsov >> wrote: >> > Hi! >> > >&g

Re: [gmx-users] Pme on gpu performance

> Will it use CUDA or OpenCL? Second one will be more common since it will > work with wider range of platfroms (cpu, gpu, fcpga) > > Szilárd Páll писал 27.11.2011 23:50: >> >> Native acceleration = not relying on external libraries. ;) >> >> -- >> Szilárd

Re: [gmx-users] Pme on gpu performance

n 2011-11-27 12:10:47PM -0600, Szilárd Páll wrote: >> Hi Andrzej, >> >> GROMACS 4.6 is work in progress, it will have native CUDA acceleration >> with multi-GPU support along a few other improvements. You can expect >> a speedup in the ballpark of 3x. We will soon hav

Re: [gmx-users] Pme on gpu performance

Hi Andrzej, GROMACS 4.6 is work in progress, it will have native CUDA acceleration with multi-GPU support along a few other improvements. You can expect a speedup in the ballpark of 3x. We will soon have the code available for testing. I'm a little skeptical about the 5x of ACEMD. What setting di

Re: [gmx-users] gromacs 4.5.3 and GCC 4.1.x

Hi, I don't remember any incident related to tools crashing, but I do recall a problem which initially was attributed to a known gcc 4.1 bug (http://redmine.gromacs.org/issues/431), but it turned out to be a GB bug. However, knowing that there is such a nasty bug in gcc 4.1, we thought it's bette

Re: [gmx-users] CygWin and Gromacs 4.5.5

On Tue, Nov 8, 2011 at 11:59 PM, Mark Abraham wrote: > On 8/11/2011 11:35 PM, Szilárd Páll wrote: > >> Hi, >> >> There have been quite some discussion on the topic of GROMACS on >> Cygwin so please search the mailing list for information. >> > >

Re: [gmx-users] CygWin and Gromacs 4.5.5

Hi, There have been quite some discussion on the topic of GROMACS on Cygwin so please search the mailing list for information. Some of that information might have not gone into the wiki (http://goo.gl/ALQuC) - especially that the page appears to be intact for the last 7 months. [Which is a pity a

Re: [gmx-users] Link to Intel MKL (fftw) via cmake options

On Mon, Oct 31, 2011 at 1:06 PM, Mark Abraham wrote: > On 30/10/2011 8:56 AM, Mirco Wahab wrote: >> >> On 24.10.2011 23:23, Szilárd Páll wrote: >>> >>> I've just realized that both you and the similar report you linked to >>> were using CMake 2.

Re: [gmx-users] Link to Intel MKL (fftw) via cmake options

ind entering it as a bug in redmine.gromacs.org. I'll look into the issue in the coming days. Cheers, -- Szilárd On Sat, Oct 29, 2011 at 11:56 PM, Mirco Wahab wrote: > On 24.10.2011 23:23, Szilárd Páll wrote: >> >> I've just realized that both you and the similar repor

Re: [gmx-users] Gromacs-GPU with an Nvidia GeForce GTX 580 error?

oint have no atoms in > VMD.  So, that's probably not a good thing. Wow, that sounds crazy. What driver version are you using? Try to update your device driver + nvidia-settings - I've been using 285.05.05/09 without problems. -- Szilárd >  Thanks, >  Matt > > On Mon,

Re: Re: [gmx-users] failure during compiling gromacs 4.5.5

Hi, > Thank you very much. I removed -xHOST from CFLAGS and FFLAGS, and now it > runs correctly. Good that it worked. Still it's bizarre that icc failed at compiling the code it generated... FYI: removing the flag might result in slightly slower binaries, but the difference should be quite small

Re: [gmx-users] Fatal error in MPI_Allreduce upon REMD restart

Hi, Firstly, you're not using the latest version and there might have been a fix for your issue in the 4.5.5 patch release. Secondly, you should check the http://redmine.gromacs.org bugtracker to see what bugs have been fixed in 4.5.5 (ideally the target version should tell). You can also just do

Re: [gmx-users] Link to Intel MKL (fftw) via cmake options

I've just realized that both you and the similar report you linked to were using CMake 2.8.3. If you don't succeed could you try another CMake version? -- Szilárd On Mon, Oct 24, 2011 at 11:14 PM, Szilárd Páll wrote: > Please keep all discussions on the mailing list! Also, I'

Re: [gmx-users] Link to Intel MKL (fftw) via cmake options

Please keep all discussions on the mailing list! Also, I'm also CC-ing to the gmx-devel list, maybe somebody over there has an better what causes your CMake issue. >>> //Flags used by the compiler during all build types >>> CMAKE_C_FLAGS:STRING=' -msse2 -ip -funroll-all-loops -std=gnu99  ' >>> >>>

Re: [gmx-users] Gromacs-GPU with an Nvidia GeForce GTX 580 error?

Hi Matt, Yes, you should use the "force-device=yes" option, the patch which was meant to update the list of compatible GPUs didn't make it for 4.5.5. Cheers, -- Szilárd On Sun, Oct 23, 2011 at 10:24 PM, Matt Larson wrote: > I am having an error trying to use a compiled mdrun-gpu on my GPU set

Re: [gmx-users] failure during compiling gromacs 4.5.5

Hi, The error messages are all referring to SSE 4.1 packed integer min/max operations not being recognized. I assume that these were enabled by the "-xHOST" compiler option, and icc automatically generated these instructions - the files it's complaining about are even temporary files. Could it be

Re: [gmx-users] Link to Intel MKL (fftw) via cmake options

> --- [CMakeCache.txt] - > > ... > > //Flags used by the compiler during all build types > CMAKE_CXX_FLAGS:STRING=' -msse2 -ip -funroll-all-loops -std=gnu99  ' > > //Flags used by the compiler during release builds. > CMAKE_CXX_FLAGS_RELEASE:STRING=-mtune

Re: [gmx-users] using gromacs with an specific GCC

Hi Nathalia, Right, gcc 4.1 is quite controversial as these is bug in it which is though to be causing mdrun crashes. So you better stay away from 4.1 as well as from other old gcc versions. I'd recommend 4.5 or 4.6 as these have gotten really good, even compared to icc - at least when it comes to

Re: [gmx-users] Gromacs: Cloud Vs. Boinc Server?

erformance point of view the 570 way better and depending on the use case even a 560 can be a decent and cheap option. -- Szilárd > On Wed, Oct 12, 2011 at 9:54 AM, Szilárd Páll wrote: >> Dear Stephan, >> >>> Radeons work as well.  You can put a 3-4 GPU board together w

Re: [gmx-users] Gromacs: Cloud Vs. Boinc Server?

Dear Stephan, > Radeons work as well.  You can put a 3-4 GPU board together with the highest > end AMD or Intel chip for 3K, plus 16G RAM if you look around for a day or > two, but the cooling is the main problem (with 1/4 the price radeons Vs. GTI > cards), so one has to take cooling into acco

Re: [gmx-users] Gromacs: Cloud Vs. Boinc Server?

Hi Gregory, I am not very familiar with the could computing offerings, but as far as I know, in general they are not a very cheap solution when it comes to relatively low usage (non massive enterprise use). If you would need it only for you own research, you might be better off with applying for

Re: [gmx-users] RE:RE: gromacs installation

Hi, Based on the message it seem that autom4te (part of the autoconf tools) can't write some temporary file to the standard temp location /tmp. That would quite strange as if the temp directory is not there $TMPDIR should be defined, but I suspect it's not, otherwise autom4te would have picked it

Re: [gmx-users] building GROMACS 4.5.4 on Power6 with CMAKE

Hi, I have not followed the entire discussion so I might be completely wrong, I might be fill in some gaps. > Firstly, including config.h inside the fortran .F kernel files for power6 is > causing problems with > their parsing using xlf. adding -WF,-qfpp didn't help. Had to provide a > modified x

Re: [gmx-users] more than 100% CPU

It is true that on Intel CPUs with HT supported and on you get an up to 10-15% speedup if you also use all virtual cores wrt to running only as many threads as real cores. Additionally, as the OS reports all virtual processors, by Gromacs will use all of them by default, i.e. will run with 8 thread

Re: [gmx-users] GROMACS with GPU

Hi, Gromacs 4.5.x works only with OpenMM 2.x. You might be able to use CUDA 4.0, but you will probably have to recompile OpenMM from source. Cheers, -- Szilárd On Fri, Aug 19, 2011 at 2:23 AM, Park, Jae Hyun nmn wrote: > Dear GMX users, > > > > I am installing GMX 4.5.3 with GPU. > > But, the

Re: [gmx-users] RE: Gromacs on GPU: GTX or Tesla?

Hi, Tesla cards won't give you much benefit when it comes to running the current Gromacs. Additionally, I can tell you so much that this won't change in the future either. The only advantage of the C20x0-s is ECC and double precision - which is ATM anyway not supported in Gromacs on GPUs. Gromacs

[gmx-users] Re: [gmx-developers] GPU

Hi, As this is not a development-related question I'm moving the discussion to the user's list. Future replies should be sent *only* to gmx-users@gromacs.org. As Axel pointed out, the list of CUDA-compatible devices is much broader than the list of cards we label compatible. The compatibility che

Re: [gmx-users] Installation of gromacs-gpu on windows

I think you made the right decision! :) -- Szilárd On Fri, Jul 8, 2011 at 12:50 PM, Андрей Гончар wrote: > Thanks a lot! > Now we decided to use gromacs under linux and the installation of > gromacs and gromacs-gpu has passed without errors > Problem is solved :) > > 201

Re: [gmx-users] Installation of gromacs-gpu on windows

how-to about step-by-step compiling of gpu-accelerated gromacs under > windows, because now i'm totally confused... Thanks in advance! > > 2011/6/30 Szilárd Páll : >> Dear Andrew, >> >> Compiling on Windows was tested only using MSVC and I have no idea if >> it works

Re: [gmx-users] Gromacs compilation on AMD multicore

Additionally, if you care about a few percent extra performance, you should use gcc 4.5 or 4.6 for compiling Gromacs as well as FFTW (unless you have a bleeding-edge OS which was built with any of these latest gcc versions). While you might not see a lot of improvement in mdrun performance (wrt gcc

Re: [gmx-users] Installation of gromacs-gpu on windows

Dear Andrew, Compiling on Windows was tested only using MSVC and I have no idea if it works or not under cygwin. You should just try, both cmake and gcc is available for cygwin so you might be lucky and get mdrun-gpu compiled without any additional effort. All binaries on the Gromacs webpage _are

Re: [gmx-users] Re: Error of installing gromacs v4.5.4

Hi, That compiler is ancient (thought it might have SSE2 support) as well as the OS, I guess (RHEL 3?). Still, the CPU does support SSE2 so if you can get a gcc 4.1 or later on it you should still be able compile and run the code without a problem. -- Szilárd 2011/5/26 Hsin-Lin Chiang : > Hi,

Re: [gmx-users] Error of installing gromacs v4.5.4

Hi Hsin-Lin, Your problem are caused by a missing header file which is included by the nobonded SSE kernels which is indicated by the first error in your output: nb_kernel400_ia32_sse.c:22:23: emmintrin.h: No such file or directory This header is needed for SSE and SSE2, but for some reason you

Re: [gmx-users] Re: Re: Re: Gromacs Installation Error on Powerbook G4 Running OS 10.5.8

Hi Matt, Just wanted to warn you that AFAIK Gromacs 4.5.x was not tested with gcc 4.0.1, we've done testing only with 4.1 and later. This doesn't mean that it shouldn't work, but if you encounter anything strange, the first thing you should do is to get a newer gcc. Also, your tMPI errors might b

Re: [gmx-users] RHEL OS, g_mdrun

Hi, You should really use fftw, it's *much* faster! (Btw: fftpack comes with Gromacs.) I'm not sure what versions of Gromacs are available through the RHEL packages, but as installing from source is not very difficult (especially for a sysadmin) you might be better of with getting a fresh install

Re: [gmx-users] P-LINCS and nstlist

> nstlist is more directly related to dt, and is often connected to the force > field, as well.  Values of 5-10 are standard.  Setting nstlist = 1 is > usually only necessary for EM, not MD.  Excessive updating of the neighbor > list can result in performance loss, I believe. Not only can, but it

Re: [gmx-users] gromacs make error

Just some hints: - Does the target platform (32/64 bit) or the fftw libs and Gromacs build match? - Try to do a make clean first and (/or?) and reconfigure with --enable-shared. Not sure that it will help, but I vaguely remember something. - Try CMake. Cheers, -- Szilárd On Tue, May 10, 2011

Re: [gmx-users] Fwd: Compiling issue : Compiling gromacs 4.5.4 with intel compiler suite 12.0 SOLVED !

Hi, Good that managed to solve the issue! Even though it might have been caused by a bug in the autoconf scripts, as these are the final days for the autoconf support in Gromacs, I see a very slim change that it will get investigated/fixed. -- Szilárd On Tue, May 10, 2011 at 4:19 PM, wrote

Re: [gmx-users] Fwd: Compiling issue : Compiling gromacs 4.5.4 with intel compiler suite 12.0

Hi, > Is there any common problem for an compilation with the intel compiler > suite 12.0 and FFTW 3.2.2/Gromacs 4.5.4 Not that I know of, I've never had/head about such issues. I just checked and I couldn't reproduce your issue. Tried with both autoconf and CMake and with: Intel Compilers: v12.

Re: [gmx-users] openmm 3.0, opencl support

Hi Claus, > be supported in future versions. Yet, in the openmm website, > the new version of openmm (3.0 that is) is supposed to support both cuda and > opencl framework alongside gromacs: > (https://simtk.org/project/xml/downloads.xml?group_id=161) What do you mean by "alongside gromacs"? > 1)

Re: [gmx-users] Modified Gromacs and OPENMM

Hi, > Thanks for the reply. The part I modified is the implicit solvent > part, particularly the Still model. Also I modified a part of nonbonded > kernel, not sse ones. So I assumed I have to link GROMACS with OPENMM > using customGBforce? You mean that you modified the CUDA kernel inside OpenMM

Re: [gmx-users] no CUDA-capable device detected

Hi Sebastian, Are you sure that the NVIDIA driver works and is compatible with the CUDA version you have? What does "nvidia-smi -L -a" output? Have you tried running something, for instance an SDK sample? Cheers, -- Szilárd 2011/4/18 SebastianWaltz : > Dear gromacs user, > > I have some proble

Re: [gmx-users] speed issue, gmx runtime estimate = f(t)

Hi, As Justin said, it's probably the imbalance which is causing the slowdown. You can take a look at the statistics at the end of the log file. One simple thing you could do is to compare the log file of your long, gradually slowing down run with a shorter run to see which part takes more time.

Re: [gmx-users] problems when installing gromacs 4.5.3 or 4.5.4 with GPU's

gt; > Jordi Inglés > > El 29/03/11 13:00, Szilárd Páll escribió: >> >> Hi, >> >> I've diff-ed the cache file you sent me against the one I generated >> and I couldn't see anything relevant. Neither does the verbose CMake >> output suggest anything

Re: [gmx-users] problems when installing gromacs 4.5.3 or 4.5.4 with GPU's

ctory: > > -rwxr-xr-x  1 root   root  3433307 Mar 29 08:31 mdrun-gpu > > I attach also the CMakeCache list if it can help. > > Thanks for any advise! > > jordi inglés > > El 28/03/11 21:50, Szilárd Páll escribió: >> >> Hi Jordi, >> >> I've never

Re: [gmx-users] problems when installing gromacs 4.5.3 or 4.5.4 with GPU's

Hi Jordi, I've never seen this error or anything similar, but I can give you hints. The CMake build system first generates binaries in the build directory which are also runnable from there (are linked against libs located in the build three). When you do a "make install[-mdrun]", howerver, these

Re: [gmx-users] no output dgdl file

> I am a bit confused on the g_bar part, when it says -f expects multiple > dhdl files. Do we need to run still multiple independent simulations > using different foreign_lambda values? I do not see why we should run > independent simulations, if we use for couple-lambda0 and couple-lambda1 > vdw-q

Re: [gmx-users] no output dgdl file

> 1- I am wondering for each interval say > > Interval 2: > init_lambda = 0.05 > foreign_lambda = 0 0.1 > > how this foreign_lambda 0 is related to the init_lambda = 0 from interval 1 > and the same for foreign_lambda = 0.1 in interval 2 and init_lambda = 0.1 in > interval 3? Is there a physical me

Re: [gmx-users] Tweeking MDP file options to run on GPU

Hi, What is the error you are getting? What is unfortunate about temperature coupling? Have you checked out the part of the documentation, especially the supported features on GPUs part (http://www.gromacs.org/gpu#Supported_features)? -- Szilárd On Mon, Mar 7, 2011 at 3:43 PM, kala wrote: >

Re: [gmx-users] mdrun-gpu

Dear Natalia, The current mdrun-gpu (which btw uses OpenMM) is capable to run a single simulation, on a single node, using a single GPU only. Cheers, -- Szilárd On Fri, Mar 4, 2011 at 6:28 PM, Nathalia Garces wrote: > Hello, > I want to know if it is possible to use "mdrun-gpu" with the comma

Re: [gmx-users] Need help troubleshooting an mdrun-gpu error message!

Hi, There are two things you should test: a) Does your NVIDIA driver + CUDA setup work? Try to run a different CUDA-based program, e.g. you can get the CUDA SDK and compile one of the simple programs like deviceQuery or bandwidthTest. b) If the above works, try to compile OpenMM from source with

Re: [gmx-users] Dell PowerEdge M710 with Intel Xeon 5667 processor

hip, your max clockrate tends to be lower. > >As such, its really important to know how your jobs are bound so that > >you can order a cluster configuration that'll be best for that job. > > > Cheers, Maryam > > --- On *Tue, 18/1/11, Szilárd Páll > > * wrote

Re: [gmx-users] Dell PowerEdge M710 with Intel Xeon 5667 processor

Hi, Although the question is a bit fuzzy, I might be able to give you a useful answer. >From what I see on the whitepaper of the Poweredge m710 baldes, among other (not so interesting :) OS-es, Dell provides the options of Red Had or SUSE Linux as factory installed OS-es. If you have any of these

Re: [gmx-users] When will FEP be on GPU?

Hi, Currently there is no concrete plan to implement FEP on GPUs. AFAIK there is an OpenMM plugin which could be integrated, but I surely don't have time to work on that and I don't know of anyone else working on it. Contribution would be welcome, though! Regards, -- Szilárd On Thu, Nov 11, 20

Re: Antw: [gmx-users] NaN error using mdrun-gpu

Hi, I've never seen/had my hands on the Tesla T10 so I didn't know that's the name it reports. I'll fix this for the next release. Rest assured that on this hardware Gromacs-GPU should run just fine. On the other hand, your driver version is very strange: CUDA Driver Version = 4243455, while it s

Re: [gmx-users] Desktop Freezes While Using mdrun-gpu

Hi Solomon, Just stumbled upon your mail and I thought you could still use a answer to your question. First of all, as you've probably read on the Gromacs-GPU page, a) you need a high-performance GPU to achieve good performance (in comparison to the CPU) -- that's the reason for the strict compat

Re: Antw: [gmx-users] NaN error using mdrun-gpu

Hi, Tesla C1060 and S1070 should is definitely supported so it's strange that you get that warning. The only thing I can think of is that for some reason the CUDA runtime reports the name of the GPUS other than C1060/S1070. Could you please run the deviceQuery from the SDK and provide the output h

Re: [gmx-users] Problem regarding Gromacs - GPU

Hi, If you take a look at the mdp file, it becomes obvious that the simulation length is infinite: nsteps = -1 This is useful for a benchmarking setup where you want to run e.g. ~10min case in which you'r use the "-maxh 0.167" mdrun option. Cheers, -- Szilárd On Tue, Nov 23, 201

Re: [gmx-users] Installing mdrun-gpu Using Gromacs-4.5.3

Hi Solomon, > [100%] Building C object src/kernel/CMakeFiles/mdrun.dir/md_openmm.c.o > Linking CXX executable mdrun-gpu > ld: warning: in /usr/local/openmm/lib/libOpenMM.dylib, file was built for > i386 which is not the architecture being linked (x86_64) The above linker message clearly states wh

Re: [gmx-users] ./mdrun-gpu fatal error

You can try the systems we provided on the GROMACS-GPU page: http://www.gromacs.org/gpu#GPU_Benchmarks -- Szilárd On Sat, Nov 6, 2010 at 12:59 AM, lin hen wrote: > Yeah, I think my problem is the input, but I don't have the .mpd file,  I am > using the existing input which has no problem with

Re: [gmx-users] installation of gromacs on windows using cygwin

Hi, If you have installed fftw3 in the standard location it whould work out of the box. Otherwise, you have to set the LDFLAGS and CPPFLAGS to the library and include location respectively. However, there's one more thing I can think of: did you make sure that you compiled fftw3 in single precisi

Re: [gmx-users] GPU slower than I7

Hi Renato, First of all, what you're seeing is pretty normal, especially that you have a CPU that is crossing the border of insane :) Why is it normal? The PME algorithms are just simply not very well not well suited for current GPU architectures. With an ill-suited algorithm you won't be able to

Re: [gmx-users] charmm tip5p in Gmx 4.5.2

Hi, > Does anyone have an idea about what time the Gmx 4.5.2 will be released? Soon, if everything goes well in a matter of days. > And in 4.5.2, would the modified tip5p.itp in charmm27 force field be the > same as that in current git version? The git branch release-4-5-patches is the branch

Re: [gmx-users] Simulations on GPU

Dear Igor, Your output look _very_ weird, it seems as if CMake internal variable(s) were not initialized, which I have no clue how could have happened - the build generator works just fine for me. The only thing I can think of is that maybe your CMakeCache is corrupted. Could you please rerun cma

[gmx-users] Re: [gmx-developers] Simulations on GPU

Hi, The beta versions are all outdated, could you please use the latest source distribution (4.5.1) instead (or git from the release-4-5-patches branch)? The instructions are here: http://www.gromacs.org/gpu#Compiling_and_custom_installation_of_GROMACS-GPU >> The requested platform "CUDA" could n

[gmx-users] Re: [gmx-developers] Simulations on GPU

I think this mail belongs to the user's list, CC-d will continue the discussion there. -- Szilárd 2010/10/5 Igor Leontyev : > Dear gmx-developers, > My first attempt to start GPU-version of gromacs has no success. The reason > is that grompp turns off setting of electrostatics overriding them b

Re: [gmx-users] an example to test mdrun-gpu x mdrun

> If using Tcoupl and Pcoupl = no and then I can compare mdrun x mdrun-gpu, > being my gpu ~2 times slower than only one core. Well, I definitely don't > intended to use mdrun-gpu but I am surprised that it performed that bad (OK, > I am using a low-end GPU, but sander_openmm seems to work fine and

Re: [gmx-users] compilation problem: gromacs 4.5 double precision

Hi David, Are you sure you're using gcc 3.4? Because if you are, I'd strongly suggest that you switch to 4.x! Cheers, -- Szilárd On Tue, Sep 14, 2010 at 5:21 PM, David Parcej wrote: > Hi all. > I have a problem building the double (but not single) precision version of > gromacs 4.5 on an AMD

Re: [gmx-users] please help, cannot compile gmx 4.5 openmm

Hi Alan, I assume this is still the same issue on the same issue (same machine/os) as you reported last time. Could you provide some details about the version of OS, compiler, CUDA, OpenMM you're using? I'll look into the problem and get back to you if I figure out something. Cheers, -- Szilárd

Re: [gmx-users] Problem about thread based MPI in Gromacs-4.5.1

Hi, > But when use "mdrun -h", the -nt does not exist. > So can the -nt option be used in mdrun? Just checked and If you have threads turned on (!) when building gromacs then on the help page (mdrun -h) -nt does show up! Otherwise, it's easy to check if you have thread-enabled build or not: just

Re: [gmx-users] Problems with CMake and shared libraries

Hi, Indeed, the custom cmake target "install-mdrun" was designed to only install the mdrun binary and it does not install the libraries this is linked against when BUILD_SHARED_LIBS=ON. I'm not completely sure that this is actually a bug, but to me it smells like one. I'll file a bug report and w

Re: [gmx-users] gmx 4.5 and openmm on Mac, still not compiling

Hi, FYI, now building the GPU accelerated version in a non-clean build tree (used to build the CPU version) should work as well as the other way around. _However_, be warned that in the latter case the CPU build-related parameters do _not_ get reset to their default values (e.g. GMX_ACCELERATION

Re: [gmx-users] FTP Server not working?

Hi Mark, I've just tried the link you mentioned and it seems to work. Could you try again? Cheers, -- Szilárd On Tue, Aug 31, 2010 at 9:53 AM, Mark Cheeseman wrote: > Hello, > > I am trying to download Version 4.0.5 but the FTP server keeps timing out. > Is there a problem? > > Thanks, > Mark

Re: [gmx-users] abnormal stop of job

Hi, The message is quite obvious about what happened: mdrun received a TERM signal and therefor it stopped (see: man 7 signal or http://linux.die.net/man/7/signal). Figuring out the reason who and why sent a TERM signal to your mdrun will be your task, but I can think of 2 basic scenarios: (I) yo

Re: [gmx-users] new beta release - gromacs-4.5-beta2

Hi, Could you provide the compiler versions you used? I really hope it's not gcc 4.1.x again... Cheers, -- Szilárd On Thu, Aug 5, 2010 at 8:26 PM, Elio Cino wrote: > > Since the charmm force field has some instances with large charge groups > (grompp warns you for it) it is advisable to use a

Re: [gmx-users] What version of cmake is required to compile v4.5b2 for GPUs?

Hi Chris, Though I'm repeating myself, for the sake of not leaving this post unanaswered (btw reposts should be avoided as much as possible!): First of all, as Rossen said, the <=2.6.4 is a typo, it was meant to be >=2.6.4, it _should_ work with 2.8.0 (I took the FindCUDA.cmake script from the 2.

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