Assemble the output files when using mpirun
******************* This email originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list https://spam.ic.ac.uk/SpamConsole/Senders.aspx to disable email stamping for this address. ******************* Dear all; When I use the mpirun command to run a solver, dependent on the number of cores, chk format files produce (e.g. *_P0.chk, *_P1.chk, *_P2.chk, ...). Is there any way to assemble all of these .chk files and reconstruct a single output file containing all domain information? Best Regards, Mohammad
Hi Mohammad, If you are using the compressed binary output format, the solver will produce a directory with each of the each of the files containing the appropriate field and information from each processor. Nektar++ utilities like FieldConvert can handle directories like this as an input. This is done for efficiency in writing the outputs – output is then not dependent on either a sequential or serial write – which would be very costly on large jobs. You can convert them to the newer HDF5 format (if you have compiled with it) by using FieldConvert i.e. FieldConvert <mesh> <session> *.chk *_hdf5.chk:out:format=Hdf5. I’ve never tried but running the command serially without the output module i.e by just loading in the new fld and dumping – may do what you’re asking – however probably not necessary and very inefficient. HDF5 will be more efficient in terms of space than compressed binary as well as just being a singular file – which is preferrable on certain file systems. You might also consider writing to HDF5 directly by including the flag -i Hdf5 in your run command. Hope this helps! Kind Regards, James. From: nektar-users-bounces@imperial.ac.uk <nektar-users-bounces@imperial.ac.uk> On Behalf Of m.r.rouhanian@ut.ac.ir Sent: Monday, November 7, 2022 12:32 AM To: nektar-users <nektar-users@imperial.ac.uk> Subject: [Nektar-users] Assemble the output files when using mpirun This email from m.r.rouhanian@ut.ac.ir<mailto:m.r.rouhanian@ut.ac.ir> originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list<https://spam.ic.ac.uk/SpamConsole/Senders.aspx> to disable email stamping for this address. Dear all; When I use the mpirun command to run a solver, dependent on the number of cores, chk format files produce (e.g. *_P0.chk, *_P1.chk, *_P2.chk, ...). Is there any way to assemble all of these .chk files and reconstruct a single output file containing all domain information? Best Regards, Mohammad
participants (2)
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                m.r.rouhanian@ut.ac.ir
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                Slaughter, James W