Message boards : News : CUDA app testing
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![]() Project administrator Project developer Project tester ![]() Send message Joined: 8 Nov 10 Posts: 125 Credit: 5,508,546 RAC: 0 ![]() |
No, you have CUDA 6.5 where 8.0 is minimum, you need to update your CUDA driver. Cuda 2.3 is "Compute capabilty" where Cuda 8.0 is driver version used in Gromacs compilation. Just CUDA capabilities are not same as CUDA runtime version... For this app CUDA 2.3 version is need with CUDA 8.0 version driver. Krzysztof 'krzyszp' Piszczek Member of Radioactive@Home project team and Universe@Home admin. |
mmonnin Send message Joined: 25 Jan 17 Posts: 34 Credit: 6,961,791 RAC: 0 ![]() |
No, you have CUDA 6.5 where 8.0 is minimum, you need to update your CUDA driver. Other projects put in the 6.5, 8.0, 9.0 number in the plan class. SETI and GPUGrid do. Thought it was that number. |
Jim1348 Send message Joined: 27 Jul 17 Posts: 27 Credit: 160,111 RAC: 2 ![]() |
Other projects put in the 6.5, 8.0, 9.0 number in the plan class. SETI and GPUGrid do. Thought it was that number. Yes, that is the way I see it on the other projects. I think more people would understand it if they said "CUDA 8.0" in the name. I don't think the "compute capability" has much meaning to most people, unless they look it up for some reason. |
JAB_au Send message Joined: 30 Sep 17 Posts: 1 Credit: 5,758,064 RAC: 1 ![]() |
Progress is lost if the task becomes paused |
![]() Project administrator Project developer Project tester ![]() Send message Joined: 8 Nov 10 Posts: 125 Credit: 5,508,546 RAC: 0 ![]() |
Progress is lost if the task becomes paused No, isn't, just at the moment checkpoints are not reported to Manager. I will update application for proper progress bar and checkpoints reporting later today. Krzysztof 'krzyszp' Piszczek Member of Radioactive@Home project team and Universe@Home admin. |
mmonnin Send message Joined: 25 Jan 17 Posts: 34 Credit: 6,961,791 RAC: 0 ![]() |
Progress is lost if the task becomes paused Progress bar is the thing that seems to work. At least I've seen it progress. Points were cut by a 1/10? |
PappaLitto Send message Joined: 19 Oct 17 Posts: 6 Credit: 284,485 RAC: 0 ![]() |
I'm having extreme difficulty getting my hands on a Gromacs application for my GPUs. Are maxwell series cards supported? If not my 980ti's would dramatically speed things up if you can include them. |
![]() Project administrator Project developer Project tester ![]() Send message Joined: 8 Nov 10 Posts: 125 Credit: 5,508,546 RAC: 0 ![]() |
In version 0.26 of gmx (for Windows) checkpoint and fraction done values are exported to wrapper. Checkpoints are created from first version just wrapper doesn't know about it. Checkpoints are done every 15 minutes. Also progress is reported every 15 minutes. Krzysztof 'krzyszp' Piszczek Member of Radioactive@Home project team and Universe@Home admin. |
Jim1348 Send message Joined: 27 Jul 17 Posts: 27 Credit: 160,111 RAC: 2 ![]() |
I'm having extreme difficulty getting my hands on a Gromacs application for my GPUs. Are maxwell series cards supported? If not my 980ti's would dramatically speed things up if you can include them. Downloading it is easy: http://manual.gromacs.org/documentation/#latest-releases The problem is getting it installed. I get an error message that home directory does not contain "CMakeLists.txt" when I follow the instructions provided on this forum. I think someone needs to do some work to get these applications ready for prime time. I have a GTX 980 that I am hoping to use too; it should work OK. |
![]() Project administrator Project developer Project tester ![]() Send message Joined: 8 Nov 10 Posts: 125 Credit: 5,508,546 RAC: 0 ![]() |
Are you exactly do what is in my instruction? This error says that probably you miss step where you need to go inside freshly created build directory (before do cmake command). Krzysztof 'krzyszp' Piszczek Member of Radioactive@Home project team and Universe@Home admin. |
Jim1348 Send message Joined: 27 Jul 17 Posts: 27 Credit: 160,111 RAC: 2 ![]() |
Are you exactly do what is in my instruction? In my home directory, I created a folder called "GROMACS", and extracted the "gromacs-2016.4" file into that folder. Then (from inside the GROMACS folder) I ran the command "cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=on -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_BUILD_SHARED_EXE=OFF" and got that error message. It appears to me that I should be inserting the name of the gromacs file somewhere in the command, but where? EDIT: I think I have found the problem. I was not extracting the "gromacs-2016.4" file properly in Ubuntu. So I did it using 7zip on my Wn7 machine, and am copying it to the Ubuntu machine. If that does not work, I will post again, with whatever error I may get, but this should get me past that problem. Thanks. EDIT 2: Also, even though I was executing the command from inside the GROMACS folder, I still had to include that folder path in the command, as follows: "cmake ../GROMACS -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=on -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_BUILD_SHARED_EXE=OFF" It seems to be compiling OK now, though I have not run it yet. |
![]() Project administrator Project developer Project tester ![]() Send message Joined: 8 Nov 10 Posts: 125 Credit: 5,508,546 RAC: 0 ![]() |
1. Unpack Gromacs2016.4 2. Inside unpacket directory create "build" folder. 3. Go inside folder created above. 4. Execute "cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=on -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_BUILD_SHARED_EXE=OFF". 6. Execute "make" command. Krzysztof 'krzyszp' Piszczek Member of Radioactive@Home project team and Universe@Home admin. |
Jim1348 Send message Joined: 27 Jul 17 Posts: 27 Credit: 160,111 RAC: 2 ![]() |
See my comment #2 below. I had to include the path to the GROMACS folder in the command, then it worked. |
![]() Project administrator Project developer Project tester ![]() Send message Joined: 8 Nov 10 Posts: 125 Credit: 5,508,546 RAC: 0 ![]() |
Not inside Gromacs folder... Inside "Gromacs2016.4/build" folder... Krzysztof 'krzyszp' Piszczek Member of Radioactive@Home project team and Universe@Home admin. |
Jim1348 Send message Joined: 27 Jul 17 Posts: 27 Credit: 160,111 RAC: 2 ![]() |
Not inside Gromacs folder... Inside "Gromacs2016.4/build" folder... I was in the GROMACS folder which contained all the extracted files when I opened the terminal. I don't see a "build" folder inside of it. So that is the problem. I should have created a "build" folder. At any rate, it has found the files and is compiling OK now. |
Jim1348 Send message Joined: 27 Jul 17 Posts: 27 Credit: 160,111 RAC: 2 ![]() |
Well still no luck. Everything seemed to compile and install correctly, at least I did not see any obvious error messages. But the first two work units failed, with a similar error message as with the earlier version of gromacs (or even before gromacs was installed?): <core_client_version>7.8.3</core_client_version> <![CDATA[ <message> process exited with code 195 (0xc3, -61)</message> <stderr_txt> 15:41:39 (2486): wrapper (7.7.26016): starting (812 +dev#, cuda_fermi) Device number read from command line: -1 15:41:40 (2486): wrapper (7.7.26016): starting (812 +dev#, cuda_fermi) 15:41:40 (2486): wrapper: running gmx (mdrun -nt 1 -deffnm md -gpu_id 0 0 ) :-) GROMACS - gmx mdrun, 2016.4 (-: GROMACS is written by: Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman Teemu Virolainen Christian Wennberg Maarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2017, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx mdrun, version 2016.4 Executable: gmx ------------------------------------------------------- Program: gmx mdrun, version 2016.4 Source file: src/gromacs/utility/path.cpp (line 241) Function: static bool gmx::Path::isEquivalent(const string&, const string&) System I/O error: Path::isEquivalent called with two invalid files Reason: No such file or directory (call to stat() returned error code 2) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- 15:41:41 (2486): gmx exited; CPU time 0.004000 15:41:41 (2486): app exit status: 0x1 15:41:41 (2486): called boinc_finish(195) </stderr_txt> ]]> |
![]() Project administrator Project developer Project tester ![]() Send message Joined: 8 Nov 10 Posts: 125 Credit: 5,508,546 RAC: 0 ![]() |
You just get failed batch, it's should fix in few minutes, when you update project (I'm working now on progress bar and checkpoint reporting). Krzysztof 'krzyszp' Piszczek Member of Radioactive@Home project team and Universe@Home admin. |
jbest Send message Joined: 4 Sep 17 Posts: 3 Credit: 220,404 RAC: 2 ![]() |
I have just disabled the use of GPU in DDH prefs as getting fed up of errors. Please advise when or if we can enable GPUs ever again for DDH WUs. Thanks. |
mikey![]() Send message Joined: 11 Mar 17 Posts: 7 Credit: 2,678,422 RAC: 6 ![]() ![]() |
I'm having extreme difficulty getting my hands on a Gromacs application for my GPUs. Are maxwell series cards supported? If not my 980ti's would dramatically speed things up if you can include them. Read this message: Message 5045 The guy has 4 980's crunching just fine, he's probably using Linux though, I didn't check but I'm not sure you need to install 'gromacs' in Windows. I didn't install it on my Windows pc's and it's crunching for me anyway, Now I may use the app-config.xml file the same guy in the above message talks about to see if it makes mine faster, some of my workunits are taking MUCH longer. |
hsdecalc Send message Joined: 11 Mar 17 Posts: 4 Credit: 3,082,947 RAC: 0 ![]() |
Gromacs 0.26 for GPU didn't use checkpoint after paused (WIN10)! After resuming a task it starts from begining, not from a checkpoint! I checked md.log and checkpoint.txt. Sample checkpoint.txt in slot 10: Writing checkpoint, step 232600 at Wed Oct 25 13:04:07 2017 After resuming at 16:30, now at 17:23: Writing checkpoint, step 198320 at Wed Oct 25 17:23:49 2017 md.log 13:04 when paused: Step Time Lambda 230000 460.00000 0.00000 ... Writing checkpoint, step 232600 at Wed Oct 25 13:04:07 2017 md.log 17:23 after one hours runtime: Step Time Lambda 195000 390.00000 0.00000 ... Writing checkpoint, step 198320 at Wed Oct 25 17:23:49 2017 Boinc-Logfile at 13:04: 25.10.2017 13:04:10 | DrugDiscovery@Home | [task] result gmx_GMX-T028_XXXX_TTTTT_tasks.gmx_20_100.in_3 checkpointed 25.10.2017 13:04:11 | DrugDiscovery@Home | [task] result gmx_GMX-T025_XXXX_TTTTT_tasks.gmx_393_1000.in_3 checkpointed 25.10.2017 13:04:16 | DrugDiscovery@Home | [task] result gmx_GMX-T030_XXXX_TTTTT_tasks.gmx_79_1000.in_3 checkpointed 25.10.2017 13:04:18 | DrugDiscovery@Home | [task] result gmx_GMX-T030_XXXX_TTTTT_tasks.gmx_27_1000.in_3 checkpointed 25.10.2017 13:08:17 | DrugDiscovery@Home | [task] result gmx_GMX-T034_XXXX_TTTTT_tasks.gmx_662_1000.in_2 checkpointed 25.10.2017 13:10:19 | DrugDiscovery@Home | task gmx_GMX-T028_XXXX_TTTTT_tasks.gmx_20_100.in_3 suspended by user 25.10.2017 13:10:19 | DrugDiscovery@Home | [cpu_sched] Preempting gmx_GMX-T028_XXXX_TTTTT_tasks.gmx_20_100.in_3 (removed from memory) 25.10.2017 13:10:19 | DrugDiscovery@Home | [task] task_state=QUIT_PENDING for gmx_GMX-T028_XXXX_TTTTT_tasks.gmx_20_100.in_3 from request_exit() 25.10.2017 13:10:19 | | request_exit(): PID 12900 has 3 descendants 25.10.2017 13:10:19 | | PID 3492 25.10.2017 13:10:19 | | PID 460 25.10.2017 13:10:19 | | PID 11624 25.10.2017 13:10:20 | DrugDiscovery@Home | [task] Process for gmx_GMX-T028_XXXX_TTTTT_tasks.gmx_20_100.in_3 exited, exit code 0, task state 8 25.10.2017 13:10:20 | DrugDiscovery@Home | [task] task_state=UNINITIALIZED for gmx_GMX-T028_XXXX_TTTTT_tasks.gmx_20_100.in_3 from handle_exited_app 25.10.2017 13:10:20 | DrugDiscovery@Home | [task] task_state=COPY_PENDING for gmx_GMX-T2008_XXXX_TTTTT_tasks.gmx_47_50.in_2 from start 25.10.2017 13:10:20 | DrugDiscovery@Home | Starting task gmx_GMX-T2008_XXXX_TTTTT_tasks.gmx_47_50.in_2 Logfile from 16:38 25.10.2017 16:38:41 | | PID 688 25.10.2017 16:38:45 | DrugDiscovery@Home | [task] task_state=COPY_PENDING for gmx_GMX-T028_XXXX_TTTTT_tasks.gmx_20_100.in_3 from start 25.10.2017 16:38:45 | DrugDiscovery@Home | [cpu_sched] Restarting task gmx_GMX-T028_XXXX_TTTTT_tasks.gmx_20_100.in_3 using gmx version 26 (cuda23) in slot 10 25.10.2017 16:38:47 | DrugDiscovery@Home | [task] task_state=EXECUTING for gmx_GMX-T028_XXXX_TTTTT_tasks.gmx_20_100.in_3 from start 25.10.2017 16:39:26 | DrugDiscovery@Home | Sending scheduler request: Requested by project. 25.10.2017 16:39:26 | DrugDiscovery@Home | Not requesting tasks: "no new tasks" requested via Manager Why it doesn´t use the checkpoint? Lose many hours of computing time. |
Message boards : News : CUDA app testing
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