Re: [gmx-users] gromacs build options

2016-10-08 Thread Mahmood Naderan
Sorry, but I got confused. I tried to follow the correct options to specify the location of libraries, bu failed... mahmood@cluster:build$ cmake .. -DCMAKE_C_COMPILER=/share/apps/computer/openmpi-2.0.1/bin/mpicc -DCMAKE_CXX_COMPILER=/share/apps/computer/openmpi-2.0.1/bin/mpic++

Re: [gmx-users] gromacs build options

2016-10-08 Thread Mahmood Naderan
​OK. I ran /share/apps/computer/cmake-3.2.3-Linux-x86_64/bin/cmake .. -DCMAKE_C_COMPILER=/share/apps/computer/openmpi-2.0.1/bin/mpicc -DCMAKE_CXX_COMPILER=/share/apps/computer/openmpi-2.0.1/bin/mpic++ -DCMAKE_PREFIX_PATH=/share/apps/chemistry/gromacs-5.1 -DBUILD_SHARED_LIBS=off please note that

Re: [gmx-users] gromacs build options

2016-10-08 Thread Mahmood Naderan
I got an error regarding fftw3. Maybe not related to GMX itself, but I appreciate any comment for that. root@cluster:build# /share/apps/computer/cmake-3.2.3-Linux-x86_64/bin/cmake .. -DCMAKE_C_COMPILER=/share/ap ps/computer/openmpi-2.0.1/bin/mpicc

Re: [gmx-users] gromacs build options

2016-10-08 Thread Mahmood Naderan
​Excuse me, what I understood from the manual is that -DCMAKE_INSTALL_PREFIX is the same as --prefix in ./configure script. Do you mean that I can give multiple location with that option? One for the gromacs itself and the other for the MPI? I mean -DCMAKE_INSTALL_PREFIX=/share/apps/gromacs-5.1

[gmx-users] gromacs build options

2016-10-08 Thread Mahmood Naderan
Hi, I am trying to install gromacs-5.1 from the source. What are the proper cmake options for the following things: 1- Installing to a custom location and not /usr/local 2- Using a customized installation of MPI and not /usr/local Regards, Mahmood -- Gromacs Users mailing list * Please search

Re: [gmx-users] gromacs build options

2016-10-08 Thread Mahmood Naderan
​OMPI-2.0.1 is installed on the system. I want to tell gromacs that mpifort (or other wrappers) are in /share/apps/openmpi-2.0.1/bin and libraries are in /share/apps/opnempi-2.0.1/lib How can I tell that to cmake? Regards, Mahmood -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Multithread run issues

2016-10-09 Thread Mahmood Naderan
Hi, Users issue the command "mdrun -v" and that will automatically read input files in the working directory. There are two issue with that which I am not aware of the solution. 1- How the number of cores can be changed? 2- Viewing the output of "top" command, it is saying that mdrun uses 400%

Re: [gmx-users] gromacs build options

2016-10-09 Thread Mahmood Naderan
for > dependencies). > > Mark > > On Sun, Oct 9, 2016 at 12:20 PM Mahmood Naderan <mahmood...@gmail.com> > wrote: > > > Hi mark, > > Thank you very much. In fact the following commands did the job > > > > > > $ cmake .. -DCMAKE_C_COMPILER=/share/ap

[gmx-users] nt/ntmpi/ntomp

2016-10-22 Thread Mahmood Naderan
Hi, What is the clear difference among nt, ntmpi and ntomp? I have built gromacs with MPI suppport. Then I run mpirun gmx_mpi mdrun Simply I want to know, is it a good idea to use 'nt' for such command? Are there some conflicts among them which degrade the performance? For example, using 'nt'

Re: [gmx-users] Switching Group to Verlet

2016-10-22 Thread Mahmood Naderan
Well such message flooding that is written in the log file at every step, the network will be a bottleneck affecting the performance of the other jobs Regards, Mahmood On Sat, Oct 22, 2016 at 3:42 PM, Mark Abraham wrote: > Hi, > > This is an energy minimization.

Re: [gmx-users] Switching Group to Verlet

2016-10-23 Thread Mahmood Naderan
Hi Mark, So I changed the code (gromacs-5.1/src/gromacs/mdlib/minimize.cpp) like this: if (MASTER(cr)) { if (bVerbose && ((++myCounter)%1==0)) { fprintf(stderr, "Step=%5d, Dmax= %6.1e nm, Epot= %12.5e Fmax= %11.5e, atom= %d%c",

Re: [gmx-users] Switching Group to Verlet

2016-10-23 Thread Mahmood Naderan
ach. That's 1.6 MB, > which you could also suppress by piping terminal output to /dev/null. The > minimization ran in around 100 seconds, so the load on the infrastructure > was under 20 kb/sec. Can you name any workload on the cluster that produces > less traffic? > > Mark > >

Re: [gmx-users] Low cpu utilization

2016-10-17 Thread Mahmood Naderan
it is interesting for me that I specified Verlet, but the log warns about group. mahmood@cluster:LPN$ grep -r cut-off . ./mdout.mdp:; cut-off scheme (group: using charge groups, Verlet: particle based cut-offs) ./mdout.mdp:; nblist cut-off ./mdout.mdp:; long-range cut-off for switched potentials

Re: [gmx-users] Low cpu utilization

2016-10-17 Thread Mahmood Naderan
​Here is what I did... I changed the cutoff-method to Verlet as suggested by http://www.gromacs.org/Documentation/Cut-off_schemes# How_to_use_the_Verlet_scheme Then I followed two scenarios: 1) On the frontend, where gromacs and openmpi have been installed, I ran ​mahmood@cluster:LPN$ date Mon

Re: [gmx-users] Switching Group to Verlet

2016-10-21 Thread Mahmood Naderan
OK. I verified that the cutoff parameter inside the trp file is Group mahmood@cluster:gromacs-5.1$ ./bin/gmx_mpi dump -s ~/LPN/topol.tpr | grep cutoff ... Note: file tpx version 83, software tpx version 103 cutoff-scheme = Group Now, according to this reply (by you Mark)

Re: [gmx-users] Switching Group to Verlet

2016-10-21 Thread Mahmood Naderan
ntion ;-) > > Mark > > On Fri, Oct 21, 2016 at 2:49 PM Mahmood Naderan <mahmood...@gmail.com> > wrote: > > > OK. I verified that the cutoff parameter inside the trp file is Group > > > > mahmood@cluster:gromacs-5.1$ ./bin/gmx_mpi dump -s ~/LPN/topol.tpr | >

Re: [gmx-users] Switching Group to Verlet

2016-10-21 Thread Mahmood Naderan
e in gmx_mpi that isn't served by mdrun_mpi. > > Mark > > On Fri, Oct 21, 2016 at 3:14 PM Mahmood Naderan <mahmood...@gmail.com> > wrote: > > > Meanwhile, I have been confused with one thing! > > If I build Gromacs with -DGMX_BUILD_MDRUN_ONLY=on, then I cannot see >

Re: [gmx-users] Switching Group to Verlet

2016-10-21 Thread Mahmood Naderan
One more question. Currently, gromacs prints the output on every step! Step= 159, Dmax= 3.8e-03 nm, Epot= -8.39592e+05 Fmax= 2.45536e+03, atom= 2111 Step= 160, Dmax= 4.6e-03 nm, Epot= -8.39734e+05 Fmax= 4.30685e+03, atom= 2111 Step= 161, Dmax= 5.5e-03 nm, Epot= -8.39913e+05 Fmax= 3.78613e+03,

[gmx-users] Switching Group to Verlet

2016-10-21 Thread Mahmood Naderan
Hi, I have specified Verlet in the mdp files according to the manual. However, as I run mdrun_mpi with ntomp switch, it says that that the cut-off is Group. mahmood@cluster:LPN$ ls *.mdp grompp.mdp md100.mdp mdout.mdp rest.mdp mahmood@cluster:LPN$ grep -r Verlet . ./grompp.mdp:cutoff-scheme

Re: [gmx-users] Switching Group to Verlet

2016-10-21 Thread Mahmood Naderan
Excuse me... this is a better output that shows the inconsistency mahmood@cluster:LPN$ grep -r cutoff . ./grompp.mdp:cutoff-scheme = Verlet ./rest.mdp:cutoff-scheme = Verlet ./md100.mdp:cutoff-scheme = Verlet ./md.log: cutoff-scheme = Group

Re: [gmx-users] Multithread run issues

2016-10-10 Thread Mahmood Naderan
Verlet For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I read that document from that web site but didn't understand what is the issue! Thanks Regards, Mahmood On Mon, Oct 10, 2016 at 2:29 PM, Mahmood Naderan

Re: [gmx-users] Multithread run issues

2016-10-10 Thread Mahmood Naderan
OK. I understood the documents. Thing that I want is to see two processes (for example) each consumes 100% cpu. The command for that is mpirun -np 2 mdrun -v -nt 1 ​Thanks Mark.​ Regards, Mahmood -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Multithread run issues

2016-10-10 Thread Mahmood Naderan
waiting for communication, but what does top think about that? > > Mark > > On Mon, Oct 10, 2016 at 11:47 AM Mahmood Naderan <mahmood...@gmail.com> > wrote: > > > OK. I understood the documents. > > Thing that I want is to see two processes (for example) ea

Re: [gmx-users] gromacs build options

2016-10-09 Thread Mahmood Naderan
Hi mark, Thank you very much. In fact the following commands did the job $ cmake .. -DCMAKE_C_COMPILER=/share/apps/computer/openmpi-2.0.1/bin/mpicc -DCMAKE_CXX_COMPILER=/share/apps/computer/openmpi-2.0.1/bin/mpic++ -DCMAKE_PREFIX_PATH=/share/apps/chemistry/gromacs-5.1 -DGMX_BUILD_OWN_FFTW=ON

[gmx-users] Low cpu utilization

2016-10-16 Thread Mahmood Naderan
Hi, A PBS script for a gromacs job has been submitted with the following content: #!/bin/bash #PBS -V #PBS -q default #PBS -j oe #PBS -l nodes=2:ppn=10 #PBS -N LPN #PBS -o /home/dayer/LPN/mdout.out cd $PBS_O_WORKDIR mpirun gromacs-5.1/bin/mdrun_mpi -v As I ssh'ed to the nodes and saw mdrun_mpi

Re: [gmx-users] Low cpu utilization

2016-10-16 Thread Mahmood Naderan
Well that is provided by nodes=2:ppn=10 in the PBS script. Regards, Mahmood On Sun, Oct 16, 2016 at 9:26 PM, Parvez Mh <parvezm...@gmail.com> wrote: > Hi, > > Where is -np option in mpirun ? > > --Masrul > > On Sun, Oct 16, 2016 at 12:45 PM, Mahmood Naderan <

Re: [gmx-users] Low cpu utilization

2016-10-16 Thread Mahmood Naderan
​>Where is -np option in mpirun ? Please see this https://mail-archive.com/users@lists.open-mpi.org/msg30043.html Regards, Mahmood -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] Low cpu utilization

2016-10-16 Thread Mahmood Naderan
Hi mark, There is a question here... What is the difference between mpirun gmx_mpi mdrun And mpirun mdrun_mpi ? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] Low cpu utilization

2016-10-17 Thread Mahmood Naderan
Problem is that I can not find out if gromacs (or MPI) is using the resources correctly. Is there any idea to see if there is any bottleneck for such low utilization? Regards, Mahmood On Mon, Oct 17, 2016 at 11:30 AM, Mahmood Naderan <mahmood...@gmail.com> wrote: > it is interesti

[gmx-users] tpr generation aborted

2018-02-24 Thread Mahmood Naderan
Hi, Following the Lusozume tutorial, I face an error at the step of generating ions.tpr which says too many warnings. $ gmx grompp -f ions.mdp -c 1AKI_solv.gro -p topol.top -o ions.tpr NOTE 1 [file ions.mdp]:   With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note   that with the

Re: [gmx-users] Minimum compute compatibility

2018-02-23 Thread Mahmood Naderan
I wrongly downloaded the v5.0. It seems that 2018 version is better! Such error is now solved. Regards, Mahmood On Friday, February 23, 2018, 4:10:15 PM GMT+3:30, Mahmood Naderan <nt_mahm...@yahoo.com> wrote: Hi,While I set -DGMX_GPU=on for a M2000 card, the make returned an

[gmx-users] Minimum compute compatibility

2018-02-23 Thread Mahmood Naderan
Hi,While I set -DGMX_GPU=on for a M2000 card, the make returned an error which says compute_20 is not supported. So, where in the options I can drop the compute_20 capability? Regards, Mahmood -- Gromacs Users mailing list * Please search the archive at

[gmx-users] cpu/gpu utilization

2018-02-26 Thread Mahmood Naderan
Hi, While the cut-off is set to Verlet and I run "gmx mdrun -nb gpu -deffnm input_md", I see that 9 threads out of total logical 16 threads are running on the cpu while the gpu is utilized. The gmx also says No option -multi Using 1 MPI thread Using 16 OpenMP threads I want to know, why 9

Re: [gmx-users] mpirun and gmx_mpi

2018-07-27 Thread Mahmood Naderan
Szillard, So, the following commands have the same meaning (8 mpi threads each 2 openmp threads as gromacs says) on an 8 core (16 threads) Ryzen CPU with one M2000. mpirun -np 8 gmx_mpi mdrun -v -deffnm nvt mpirun -np 8 gmx_mpi mdrun -v -ntomp 2 -deffnm nvt Both have 8 GPU tasks. However,

[gmx-users] gromacs with mps

2018-07-27 Thread Mahmood Naderan
Hi Has anyone run gmx_mpi with MPS? Even with small input files (which are working fine when MPS is turned off), I get out of memory error from the GPU device. Don't know if there is a bug inside cuda or gromacs. I see some other related topics for other programs. So, it sound like a cuda

Re: [gmx-users] GROMACS 2018.2 mdrun GPU Assertion failed: Condition: cudaSuccess == cudaPeekAtLastError()

2018-08-10 Thread Mahmood Naderan
>Assertion failed: >Condition: cudaSuccess == cudaPeekAtLastError() >We promise to return with clean CUDA state! Hi, I had some runtime problems with cuda 9.1 which were solved by 9.2!So, I suggest you to first update 9.0 to 9.2 and then spend time in case you get any error. Regards, Mahmood

Re: [gmx-users] mpirun and gmx_mpi

2018-07-25 Thread Mahmood Naderan
It is stated that mpirun -np 4 gmx mdrun -ntomp 6 -nb gpu -gputasks 00 Starts gmx mdrun on a machine with two nodes, usingfour total ranks, each rank with six OpenMP threads,and both ranks on a node sharing GPU with ID 0. Questions are: 1- Why gmx_mpi is not used? 2- How two nodes were

Re: [gmx-users] mpirun and gmx_mpi

2018-07-24 Thread Mahmood Naderan
No idea? Those who use GPU, which command do they use? gmx or gmx_mpi? Regards, Mahmood On Wednesday, July 11, 2018, 11:46:06 AM GMT+4:30, Mahmood Naderan wrote: Hi,Although I have read the manual and I have wrote programs with mpi, the gromacs use of mpi is confusing

[gmx-users] Optimal pme grid

2018-08-31 Thread Mahmood Naderan
Hi It seems that changing the number of ntmpi and ntomp affects the number of steps that takes to calculate the optimal pme grid. Is that correct? Please see the following output gmx mdrun -nb gpu -ntmpi 1 -ntomp 16 -v -deffnm nvt Using 1 MPI thread Using 16 OpenMP threads step 2400: timed

Re: [gmx-users] cpu threads in a gpu run

2018-07-09 Thread Mahmood Naderan
application clocks manually. Is the behavior I see, related to this note? I doubt, but if someone has a comment, I appreciate that. Regards, Mahmood On Monday, July 9, 2018, 3:13:20 PM GMT+4:30, Mahmood Naderan wrote: Hi, When I run "-nt 16 -nb cpu", I see nearly

[gmx-users] pme grid with gpu

2018-07-10 Thread Mahmood Naderan
Hi, When I run mdrun with "-nb gpu", I see the following output starting mdrun 'Protein' 2 steps, 40.0 ps. step  200: timed with pme grid 64 80 60, coulomb cutoff 1.000: 3340.0 M-cycles step  400: timed with pme grid 60 72 56, coulomb cutoff 1.075: 3742.2 M-cycles step  600: timed with

[gmx-users] Any configuration for enabling thread-MPI?

2018-07-10 Thread Mahmood Naderan
Hi, The manual says: GROMACS can run in parallel on multiple cores of a singleworkstation using its built-in thread-MPI. No user action is requiredin order to enable this. However, that may not be correct because I get this error Command line:   gmx_mpi mdrun -v -ntmpi 2 -ntomp 4 -nb gpu

[gmx-users] mpirun and gmx_mpi

2018-07-11 Thread Mahmood Naderan
Hi,Although I have read the manual and I have wrote programs with mpi, the gromacs use of mpi is confusing. Is it mandatory to use mpirun before gmx_mpi or not? Can someone shed a light on that? Regards, Mahmood -- Gromacs Users mailing list * Please search the archive at

[gmx-users] cpu threads in a gpu run

2018-07-09 Thread Mahmood Naderan
Hi, When I run "-nt 16 -nb cpu", I see nearly 1600% cpu utilization. However, when I run "-nt 16 -nb gpu", I see about 600% cpu utilization. Is there any reason about that? I want to know with the cpu threads in a gpu run is controllable. Regards, Mahmood -- Gromacs Users mailing list *

[gmx-users] computation/memory modifications

2018-03-09 Thread Mahmood Naderan
Hi, I want to do some tests on the lysozyme tutorial. Assume that the tutorial with the default parameters which is run for 10ps, takes X seconds wall clock time. If I want to increase the wall clock time, I can simply run for 100ps. However, that is not what I want. I want to increase the

Re: [gmx-users] cpu/gpu utilization

2018-02-28 Thread Mahmood Naderan
>Additionally, you still have not provided the *mdrun log file* I requested. >top output is not what I asked for. See the attached file. Regards, Mahmood -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

Re: [gmx-users] cpu/gpu utilization

2018-02-28 Thread Mahmood Naderan
>The list does not accept attachments, so please use a file sharing or content >sharing website so >everyone can see your data and has the context. I uploaded here https://pastebin.com/RCkkFXPx Regards, Mahmood -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Backup files

2018-02-28 Thread Mahmood Naderan
:50 PM András Ferenc WACHA <wacha.and...@ttk.mta.hu> wrote: Dear Mahmood, as far as I know, each command supports the "-nobackup" command line switch... Best regards, Andras On 02/28/2018 04:46 PM, Mahmood Naderan wrote: > Hi,How can I disable the backup feature? I mean backed up

Re: [gmx-users] cpu/gpu utilization

2018-02-28 Thread Mahmood Naderan
>(try the other parallel modes) Do you mean OpenMP and MPI? >- as noted above try offloading only the nonbondeds (or possibly the hybrid >PME mode -pmefft cpu) May I know how? Which part of the documentation says about that? Regards, Mahmood -- Gromacs Users mailing list * Please search

Re: [gmx-users] cpu/gpu utilization

2018-03-01 Thread Mahmood Naderan
>- as noted above try offloading only the nonbondeds (or possibly the hybrid >PME mode -pmefft cpu) So, with "-pmefft cpu", I don't see any good impact!See the log at https://pastebin.com/RTYaKSne I will use other options to see the effect. Regards, Mahmood -- Gromacs Users mailing list

Re: [gmx-users] cpu/gpu utilization

2018-03-01 Thread Mahmood Naderan
>Again, first and foremost, try running PME on the CPU, your 8-core Ryzen will >be plenty fast for that. Since I am a computer guy and not a chemist, the question may be noob! What do you mean exactly by running pme on cpu? You mean "-nb cpu"? or you mean setting cut-off to Group instead of

Re: [gmx-users] computation/memory modifications

2018-03-13 Thread Mahmood Naderan
No idea? Any feedback is appreciated. Regards, Mahmood On Friday, March 9, 2018, 9:47:33 PM GMT+3:30, Mahmood Naderan <nt_mahm...@yahoo.com> wrote: Hi, I want to do some tests on the lysozyme tutorial. Assume that the tutorial with the default parameters which is run for 10ps,

Re: [gmx-users] computation/memory modifications

2018-03-13 Thread Mahmood Naderan
KI) and follow the same procedure? Generally, the type of my questions are like those. Regards, Mahmood On Tuesday, March 13, 2018, 2:48:35 PM GMT+3:30, Justin Lemkul <jalem...@vt.edu> wrote: On 3/13/18 2:49 AM, Mahmood Naderan wrote: > No idea? Any feedback is apprec

[gmx-users] Backup files

2018-02-28 Thread Mahmood Naderan
Hi,How can I disable the backup feature? I mean backed up files which start and end with # character. Regards, Mahmood -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] Backup files

2018-02-28 Thread Mahmood Naderan
Yes you are right. Thank you very much. Regards, Mahmood On Wednesday, February 28, 2018, 7:19:55 PM GMT+3:30, András Ferenc WACHA wrote: Dear Mahmood, as far as I know, each command supports the "-nobackup" command line switch... Best regards, Andras

Re: [gmx-users] cpu/gpu utilization

2018-02-28 Thread Mahmood Naderan
  application clocks of the detected Quadro M2000 GPU to improve performance. Regards, Mahmood On Wednesday, February 28, 2018, 7:15:13 PM GMT+3:30, Mahmood Naderan <nt_mahm...@yahoo.com> wrote: By runing gmx mdrun -nb gpu -deffnm md_0_1 I see the following outputs $ top -b  | h

Re: [gmx-users] cpu/gpu utilization

2018-02-28 Thread Mahmood Naderan
By runing gmx mdrun -nb gpu -deffnm md_0_1 I see the following outputs $ top -b  | head -n 10 top - 19:14:10 up 7 min,  1 user,  load average: 4.54, 1.40, 0.54 Tasks: 344 total,   1 running, 343 sleeping,   0 stopped,   0 zombie %Cpu(s):  7.1 us,  0.5 sy,  0.0 ni, 91.9 id,  0.4 wa,  0.0 hi,  0.0

Re: [gmx-users] cpu/gpu utilization

2018-03-02 Thread Mahmood Naderan
Command is "gmx mdrun -nobackup -pme cpu -nb gpu -deffnm md_0_1" and the log says R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G On 1 MPI rank, each using 16 OpenMP threads  Computing:  Num   Num  Call    Wall time Giga-Cycles Ranks

Re: [gmx-users] cpu/gpu utilization

2018-03-01 Thread Mahmood Naderan
If you mean [1], then yes I read that and that recommends to use Verlet for the new algorithm depicted in  figures. At least that is my understanding about offloading. If I read the wrong document or you mean there is also some other options, please let me know. [1]

Re: [gmx-users] cpu/gpu utilization

2018-03-02 Thread Mahmood Naderan
Sorry for the confusion. My fault... I saw my previous post and found that I missed something. In fact, I couldn't run "-pme gpu". So, once again, I ran all the commands and uploaded the log files gmx mdrun -nobackup -nb cpu -pme cpu -deffnm md_0_1 https://pastebin.com/RNT4XJy8 gmx mdrun

[gmx-users] About GMX_PRINT_DEBUG_LINES

2019-01-17 Thread Mahmood Naderan
Hi, I set GMX_PRINT_DEBUG_LINE before the mdrun command, however, I don't see any debug message $ GMX_PRINT_DEBUG_LINES=1 $ gmx mdrun -nb gpu -ntmpi 8 -ntomp 1 -v -deffnm nvt ...NOTE: DLB can now turn on, when beneficialstep 1100, will finish Fri Jan 18 19:24:07 2019imb F  8% step 1200 Turning

[gmx-users] About fprintf and debugging

2019-01-28 Thread Mahmood Naderan
Hi Where should I set the flag in order to see the fprintf statements like     if (debug)     {     fprintf(debug, "PME: number of ranks = %d, rank = %d\n",     cr->nnodes, cr->nodeid); Any idea? Regards, Mahmood -- Gromacs Users mailing list * Please search the

[gmx-users] Cannot run short-ranged nonbonded interactions on a GPU

2019-09-08 Thread Mahmood Naderan
Hi With the following config command cmake .. -DGMX_GPU=on -DCMAKE_INSTALL_PREFIX=`pwd`/../single -DGMX_BUILD_OWN_FFTW=ON I get the following error for "gmx mdrun -nb gpu -v -deffnm inp_nvp" Fatal error: Cannot run short-ranged nonbonded interactions on a GPU because there is none detected.

[gmx-users] cmake fails with custom gcc version

2019-11-02 Thread Mahmood Naderan
Hi, Although I have specified a custom CC and CXX path, the cmake command fails with an error. $ cmake .. -DGMX_GPU=on -DCMAKE_INSTALL_PREFIX=../single61 -DGMX_BUILD_OWN_FFTW=ON -DGMX_CUDA_TARGET_SM=61 -DCMAKE_C_COMPILER=/home/mahmood/tools/gcc-6.1.0/bin/gcc

[gmx-users] Changing the default cuda path

2019-10-19 Thread Mahmood Naderan
Hi, I see this line in the cmake output -- Found CUDA: /usr/local/cuda (found suitable version "10.0", minimum required is "7.0") and I would like to change that default path to somewhere else. May I know how to do that? Regards, Mahmood -- Gromacs Users mailing list * Please search the

[gmx-users] c2075 is not detected by gmx

2019-11-24 Thread Mahmood Naderan
Hi I have build 2018.3 in order to test that with c2075 GPU. I used this command to build it $ cmake .. -DGMX_GPU=on -DCMAKE_INSTALL_PREFIX=../single -DGMX_BUILD_OWN_FFTW=ON $ make $ make install I have to say that the device is detected according to deviceQuery. However, when I run $ gmx

[gmx-users] C2075 not detected by gmx 2018.3

2019-11-24 Thread Mahmood Naderan
Hi I have built 2018.3 with the following command in order to test that with c2075 $ cmake .. -DGMX_GPU=on -DCMAKE_INSTALL_PREFIX=../single -DGMX_BUILD_OWN_FFTW=ON While deviceQuery shows the device properly, when I run $ gmx mdrun -nb gpu -v -deffnm nvt I get this error Fatal error: Cannot

Re: [gmx-users] c2075 is not detected by gmx

2019-11-24 Thread Mahmood Naderan
>Did you install the CUDA toolbox and drivers ?  >What is the output from "nvidia-smi" ? Yes it is working. Please see the full output below $ nvidia-smi Mon Nov 25 08:53:22 2019    +--+    | NVIDIA-SMI 352.99

[gmx-users] Compile for sm_20

2019-11-24 Thread Mahmood Naderan
Hi, I would like to know what is the last gromacs version that supports sm_20?I can recursively find that with try and error. But maybe somewhere that is pointed out. Regards, Mahmood -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] cmake fails with custom gcc version

2019-11-04 Thread Mahmood Naderan
-02 kl. 14:25, skrev Mahmood Naderan: > Hi, > Although I have specified a custom CC and CXX path, the cmake command fails > with an error. > > $ cmake .. -DGMX_GPU=on -DCMAKE_INSTALL_PREFIX=../single61 > -DGMX_BUILD_OWN_FFTW=ON -DGMX_CUDA_TARGET_SM=61 > -DCMAKE_C_COMPILER=/h

[gmx-users] Cannot run short-ranged nonbonded interactions on a GPU because there is none detected.

2020-04-11 Thread Mahmood Naderan
Hi Although I have built gromacs for 1080Ti and the device is working properly, I get this error when running gmx command $ ./gromacs-2019.4-1080ti/single/bin/gmx mdrun -nb gpu -v -deffnm nvt_5k  . GROMACS:  gmx mdrun, version 2019.4 Executable:  

[gmx-users] Disabling MKL

2020-04-17 Thread Mahmood Naderan
Hi How can I disable MKL while building gromacs? With this configure command cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=on  -DGMX_FFT_LIBRARY=fftw3 I see -- The GROMACS-managed build of FFTW 3 will configure with the following optimizations: --enable-sse2;--enable-avx;--enable-avx2 -- Using