Calculating memory for a job
Hi everyone, How would I go about calculating the memory requirements necessary for a particular job? I have a 23k cell mesh problem, that keeps getting deleted from my cluster because of exceeding memory usage requirements. Sincerely, -- *Amitvikram Dutta* *MASc Candidate* *Graduate Research Assistant * *Okanagan CFD Laboratory* *University of British Columbia | Okanagan Campus*
Hi, I do not believe we have a fixed mechanism. Are you sure your executable is compiled appropriately for parallel execution since if not it could be trying to run a serial job on all processors. One way to check this is whether there is a directory called infile_xml which is generated if you have an input file called infile.xml Regards, Spencer. On 31 May 2016, at 23:43, Amitvikram Dutta <amitvdutta23@gmail.com<mailto:amitvdutta23@gmail.com>> wrote: Hi everyone, How would I go about calculating the memory requirements necessary for a particular job? I have a 23k cell mesh problem, that keeps getting deleted from my cluster because of exceeding memory usage requirements. Sincerely, -- Amitvikram Dutta MASc Candidate Graduate Research Assistant Okanagan CFD Laboratory University of British Columbia | Okanagan Campus _______________________________________________ Nektar-users mailing list Nektar-users@imperial.ac.uk<mailto:Nektar-users@imperial.ac.uk> https://mailman.ic.ac.uk/mailman/listinfo/nektar-users Spencer Sherwin McLaren Racing/Royal Academy of Engineering Research Chair, Professor of Computational Fluid Mechanics, Department of Aeronautics, Imperial College London South Kensington Campus London SW7 2AZ s.sherwin@imperial.ac.uk<mailto:s.sherwin@imperial.ac.uk> +44 (0) 20 759 45052
Hi, I do not believe we have a fixed mechanism. Are you sure your executable is compiled appropriately for parallel execution since if not it could be trying to run a serial job on all processors. One way to check this is whether there is a directory called infile_xml which is generated if you have an input file called infile.xml Regards, Spencer. On 31 May 2016, at 23:43, Amitvikram Dutta <amitvdutta23@gmail.com<mailto:amitvdutta23@gmail.com>> wrote: Hi everyone, How would I go about calculating the memory requirements necessary for a particular job? I have a 23k cell mesh problem, that keeps getting deleted from my cluster because of exceeding memory usage requirements. Sincerely, -- Amitvikram Dutta MASc Candidate Graduate Research Assistant Okanagan CFD Laboratory University of British Columbia | Okanagan Campus _______________________________________________ Nektar-users mailing list Nektar-users@imperial.ac.uk<mailto:Nektar-users@imperial.ac.uk> https://mailman.ic.ac.uk/mailman/listinfo/nektar-users Spencer Sherwin McLaren Racing/Royal Academy of Engineering Research Chair, Professor of Computational Fluid Mechanics, Department of Aeronautics, Imperial College London South Kensington Campus London SW7 2AZ s.sherwin@imperial.ac.uk<mailto:s.sherwin@imperial.ac.uk> +44 (0) 20 759 45052
Hi Spencer, I checked, and the infile_xml directory is not being generated. When you refer to proper compilation of the executable, do you mean the use of the mpirun command while running the .xml file, or is there an additional step required while installing nektar++ itself? As far as I can understand from the user guide, the procedure to run a job in parallel does not involve changing any settings in the .xml file. One simply uses the miprun command and specifies the number of processors to use, and this is how I have been running my jobs. (I'm using v4.2.0) SIncerely, On Sun, Jun 5, 2016 at 7:57 AM Sherwin, Spencer J <s.sherwin@imperial.ac.uk> wrote:
Hi,
I do not believe we have a fixed mechanism. Are you sure your executable is compiled appropriately for parallel execution since if not it could be trying to run a serial job on all processors. One way to check this is whether there is a directory called infile_xml which is generated if you have an input file called infile.xml
Regards, Spencer.
On 31 May 2016, at 23:43, Amitvikram Dutta <amitvdutta23@gmail.com> wrote:
Hi everyone,
How would I go about calculating the memory requirements necessary for a particular job? I have a 23k cell mesh problem, that keeps getting deleted from my cluster because of exceeding memory usage requirements.
Sincerely, --
*Amitvikram Dutta*
*MASc Candidate*
*Graduate Research Assistant *
*Okanagan CFD Laboratory*
*University of British Columbia | Okanagan Campus*
_______________________________________________
Nektar-users mailing list Nektar-users@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/nektar-users
Spencer Sherwin McLaren Racing/Royal Academy of Engineering Research Chair, Professor of Computational Fluid Mechanics, Department of Aeronautics, Imperial College London South Kensington Campus London SW7 2AZ
s.sherwin@imperial.ac.uk +44 (0) 20 759 45052
--
*Amitvikram Dutta* *MASc Candidate* *Graduate Research Assistant * *Okanagan CFD Laboratory* *University of British Columbia | Okanagan Campus*
Hi, You have to first compile Nektar++ with MPI turned on. Now that you mention this i do not believe we have these details mentioned in the user guide. It is not always very straightforward since it depends on how your parallel machine is configured. However there are a few blogs on the web page discussing how we have set up compilation on a few of the machines we run in parallel. Have a look at the Blogs on the Nektar web page. There is a discussion on running Netkar++ on the Cray xc30 and XE6. Cheers, Spencer. On 5 Jun 2016, at 18:20, Amitvikram Dutta <amitvdutta23@gmail.com<mailto:amitvdutta23@gmail.com>> wrote: Hi Spencer, I checked, and the infile_xml directory is not being generated. When you refer to proper compilation of the executable, do you mean the use of the mpirun command while running the .xml file, or is there an additional step required while installing nektar++ itself? As far as I can understand from the user guide, the procedure to run a job in parallel does not involve changing any settings in the .xml file. One simply uses the miprun command and specifies the number of processors to use, and this is how I have been running my jobs. (I'm using v4.2.0) SIncerely, On Sun, Jun 5, 2016 at 7:57 AM Sherwin, Spencer J <s.sherwin@imperial.ac.uk<mailto:s.sherwin@imperial.ac.uk>> wrote: Hi, I do not believe we have a fixed mechanism. Are you sure your executable is compiled appropriately for parallel execution since if not it could be trying to run a serial job on all processors. One way to check this is whether there is a directory called infile_xml which is generated if you have an input file called infile.xml Regards, Spencer. On 31 May 2016, at 23:43, Amitvikram Dutta <amitvdutta23@gmail.com<mailto:amitvdutta23@gmail.com>> wrote: Hi everyone, How would I go about calculating the memory requirements necessary for a particular job? I have a 23k cell mesh problem, that keeps getting deleted from my cluster because of exceeding memory usage requirements. Sincerely, -- Amitvikram Dutta MASc Candidate Graduate Research Assistant Okanagan CFD Laboratory University of British Columbia | Okanagan Campus _______________________________________________ Nektar-users mailing list Nektar-users@imperial.ac.uk<mailto:Nektar-users@imperial.ac.uk> https://mailman.ic.ac.uk/mailman/listinfo/nektar-users Spencer Sherwin McLaren Racing/Royal Academy of Engineering Research Chair, Professor of Computational Fluid Mechanics, Department of Aeronautics, Imperial College London South Kensington Campus London SW7 2AZ s.sherwin@imperial.ac.uk<mailto:s.sherwin@imperial.ac.uk> +44 (0) 20 759 45052 -- Amitvikram Dutta MASc Candidate Graduate Research Assistant Okanagan CFD Laboratory University of British Columbia | Okanagan Campus Spencer Sherwin McLaren Racing/Royal Academy of Engineering Research Chair, Professor of Computational Fluid Mechanics, Department of Aeronautics, Imperial College London South Kensington Campus London SW7 2AZ s.sherwin@imperial.ac.uk<mailto:s.sherwin@imperial.ac.uk> +44 (0) 20 759 45052
Thanks, I'll check them out. On Sun, Jun 5, 2016, 12:12 PM Sherwin, Spencer J <s.sherwin@imperial.ac.uk> wrote:
Hi,
You have to first compile Nektar++ with MPI turned on. Now that you mention this i do not believe we have these details mentioned in the user guide. It is not always very straightforward since it depends on how your parallel machine is configured. However there are a few blogs on the web page discussing how we have set up compilation on a few of the machines we run in parallel.
Have a look at the Blogs on the Nektar web page. There is a discussion on running Netkar++ on the Cray xc30 and XE6.
Cheers, Spencer.
On 5 Jun 2016, at 18:20, Amitvikram Dutta <amitvdutta23@gmail.com> wrote:
Hi Spencer,
I checked, and the infile_xml directory is not being generated.
When you refer to proper compilation of the executable, do you mean the use of the mpirun command while running the .xml file, or is there an additional step required while installing nektar++ itself? As far as I can understand from the user guide, the procedure to run a job in parallel does not involve changing any settings in the .xml file. One simply uses the miprun command and specifies the number of processors to use, and this is how I have been running my jobs. (I'm using v4.2.0)
SIncerely,
On Sun, Jun 5, 2016 at 7:57 AM Sherwin, Spencer J < s.sherwin@imperial.ac.uk> wrote:
Hi,
I do not believe we have a fixed mechanism. Are you sure your executable is compiled appropriately for parallel execution since if not it could be trying to run a serial job on all processors. One way to check this is whether there is a directory called infile_xml which is generated if you have an input file called infile.xml
Regards, Spencer.
On 31 May 2016, at 23:43, Amitvikram Dutta <amitvdutta23@gmail.com> wrote:
Hi everyone,
How would I go about calculating the memory requirements necessary for a particular job? I have a 23k cell mesh problem, that keeps getting deleted from my cluster because of exceeding memory usage requirements.
Sincerely, --
*Amitvikram Dutta*
*MASc Candidate*
*Graduate Research Assistant *
*Okanagan CFD Laboratory*
*University of British Columbia | Okanagan Campus*
_______________________________________________
Nektar-users mailing list Nektar-users@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/nektar-users
Spencer Sherwin McLaren Racing/Royal Academy of Engineering Research Chair, Professor of Computational Fluid Mechanics, Department of Aeronautics, Imperial College London South Kensington Campus London SW7 2AZ
s.sherwin@imperial.ac.uk +44 (0) 20 759 45052
--
*Amitvikram Dutta*
*MASc Candidate*
*Graduate Research Assistant *
*Okanagan CFD Laboratory*
*University of British Columbia | Okanagan Campus*
Spencer Sherwin McLaren Racing/Royal Academy of Engineering Research Chair, Professor of Computational Fluid Mechanics, Department of Aeronautics, Imperial College London South Kensington Campus London SW7 2AZ
s.sherwin@imperial.ac.uk +44 (0) 20 759 45052
--
*Amitvikram Dutta* *MASc Candidate* *Graduate Research Assistant * *Okanagan CFD Laboratory* *University of British Columbia | Okanagan Campus*
participants (2)
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Amitvikram Dutta
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Sherwin, Spencer J