Dear Sir,
How much working memory is needed to run the tasks in MEG Pipeline , Most often i am incurring following error *" Out of memory. Type HELP MEMORY for your options.Error in ft_read_cifti (line 362)Error in megconnectome (line 129) "* I have 14.5 GB as Linux Swap Space, and 3.9 GB RAM *" vasudev@vasudev-OptiPlex-780:~$ grep MemTotal /proc/meminfoMemTotal: 3916512 kB "* Could you please let me know if it is sufficient to run the pipelines ?. Thanks Vasudev On 24 May 2016 at 20:34, Timothy B. Brown <[email protected]> wrote: > You will then need to learn how to write a script to be submitted to the > SLURM scheduler. > > I am not familiar with the SLURM scheduler, but from very briefly looking > at the documentation that you supplied a link to, I would think that the > general form of a script for the SLURM scheduler would be: > > #!/bin/bash > # ... SLURM Scheduler directives ... e.g. #SBATCH ... telling the system > such things as how much memory to expect to use > # and how long you > expect the job to take to run > # ... initialization of the modules system ... e.g. source > /etc/profile.d/modules.sh > # ... loading of the required software modules ... e.g. module load fsl > ... command to run the HCP Pipeline Script you want to run (e.g. > Structural Preprocessing, MEG processing, etc.) for the subject and scans > you want to process > > Once you've written such a script, (for example named myjob.cmd), it > appears that you would submit the job using a command like: > > sbatch myjob.cmd > > At the link that you provided, there is a section titled "Introductory > Articles and Tutorials by LRZ" I would suggest you follow the links > provided in that section, read that documentation, and submit any questions > you have to the service desk for the LRZ (a link to the service desk is > also on the page you supplied a link to.) > > Tim > > On Tue, May 24, 2016, at 13:00, Dev vasu wrote: > > Dear Sir, > > I have the cluster available , following is the link to it : > http://www.lrz.de/services/compute/linux-cluster/ > > > Thanks > Vasudev > > > > > > On 24 May 2016 at 19:43, Timothy B. Brown <[email protected]> wrote: > > Do you already have a cluster set up and available, or are you looking to > set up the cluster? > > If you are looking to set up a cluster, do you have the group of machines > that you want to use for the cluster already available or are you thinking > of setting up a cluster "in the cloud" (e.g. a group of Amazon EC2 > instances)? > > Tim > > On Tue, May 24, 2016, at 12:18, Dev vasu wrote: > > Dear Sir, > > Currently i am running HCP Pipelines on a Standalone computer but i would > like to set up the pipeline on a Linux cluster, if possible could you > please provide me some details concerning procedures that i have to follow . > > > > Thanks > Vasudev > > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > -- > Timothy B. Brown > Business & Technology Application Analyst III > Pipeline Developer (Human Connectome Project) > tbbrown(at)wustl.edu > ________________________________________ > The material in this message is private and may contain Protected > Healthcare Information (PHI). > If you are not the intended recipient, be advised that any unauthorized > use, disclosure, copying > or the taking of any action in reliance on the contents of this > information is strictly prohibited. > If you have received this email in error, please immediately notify the > sender via telephone or > return mail. > > -- > Timothy B. Brown > Business & Technology Application Analyst III > Pipeline Developer (Human Connectome Project) > tbbrown(at)wustl.edu > ________________________________________ > The material in this message is private and may contain Protected > Healthcare Information (PHI). > If you are not the intended recipient, be advised that any unauthorized > use, disclosure, copying > or the taking of any action in reliance on the contents of this > information is strictly prohibited. > If you have received this email in error, please immediately notify the > sender via telephone or > return mail. > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
