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software:ansys-fluent:ansys-fluent [2018-03-05 13:44] – [Submitting job] sraskarsoftware:ansys-fluent:ansys-fluent [2018-04-25 13:46] (current) – [Additional Resources] sraskar
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 +====== ANSYS FLUENT in batch ======
  
 +ANSYS FLUENT is commercial software that may only be used by research groups running a private license server.  You must know the port and license server name to run this example. 
 +
 +===== Submitting job =====
 +
 +
 +Copy a Grid Engine script file and all necessary input files to your working directory, and then
 +
 +  - Login headnode.
 +  - Start workgroup shell.
 +  - Change to your working directory.
 +  - Submit the job.
 +
 +<note tip>
 +Sample commands here demonstrate example for : (cluster ''mills.hpc'', user ''traine'' in workgroup ''it_css''). However, same commands are also applicable for cluster ''farber''
 +</note>
 +
 +<code>
 +ssh traine@mills.hpc.udel.edu
 +workgroup -g it_css
 +cd /lustre/work/it_css/users/traine/fluent
 +qsub fluent-3ddp.qs
 +</code>
 +
 +The working directory ''/lustre/work/it_css/users/traine/fluent'' has the
 +Grid Engine script file ''fluent-3ddp.qs'' that starts FLUENT with the input file with instructions to read the case file, run a solver and write the solution data file. FLUENT's log files, data files and script output files will be stored in the working directory after the job completes.
 +===== Downloading example =====
 +
 +An example that shows how to submit a batch mpi job to execute fluent 3ddp with an input journal file can be downloaded from
 +the link: [[http://www.udel.edu/it/research/files/cluster/fluent-3ddp-mpi.tar.gz|fluent-3ddp-mpi.tar.gz]]. 
 +
 +On Mills, the commands
 +<code bash>
 +wget http://www.udel.edu/it/research/files/cluster/fluent-3ddp-mpi.tar.gz
 +tar -zxf fluent-3ddp-mpi.tar.gz
 +</code>
 +will get and extract the files to the directory ''fluent-3ddp-mpi'', with the files:
 +  - **''fluent-3ddp.qs''** — Grid Engine script to execute ''fluent 3ddp'' with input file: ''input-3d''
 +  - **''input-3d''** — Fluent journal input files with the command to read ''3d.cas''
 +  - **''3d.cas''** — Fluent case file.
 +
 +<note important>
 +ANSYS/fluent is a licensed product, so you must export a valid value of the ''ANSYSLMD_LICENSE_FILE'' variable to gain access to fluent on Mills.
 +The exact value should be obtained from the owner of the license.  Without a proper value, the script output will contain a message such as:
 +<code text>
 +ANSYS LICENSE MANAGER ERROR:Could not connect to any license server. 
 +The server is down or is not responsive. 
 +</code>
 +</note>
 +
 +===== Running example =====
 +
 +Sample session from login to submission:
 +<code text>
 +wombat:~ jdoe$ ssh traine@mills.hpc.udel.edu
 +
 +............................................................
 +
 +    Mills cluster (mills.hpc.udel.edu)
 +
 +    This computer system is maintained by University of
 +    Delaware IT.  Links to documentation and other online
 +    resources can be found at:
 +
 +      http://docs.hpc.udel.edu/
 +
 +    For support, please contact consult@udel.edu
 +
 +............................................................
 +
 +Last login: Mon Oct  1 15:50:17 2012 from wombat.us.udel.edu
 +</code>
 +
 +<code text>
 +[traine@mills ~]$ cd /lustre/work/it_css/users/traine
 +</code>
 +<code text>
 +[traine@mills traine]$ wget http://www.udel.edu/it/research/files/cluster/fluent-3ddp-mpi.tar.gz
 +--2012-10-01 15:46:12--  http://www.udel.edu/it/research/files/cluster/fluent-3ddp-mpi.tar.gz
 +Resolving www.udel.edu... 128.175.13.63
 +Connecting to www.udel.edu|128.175.13.63|:80... connected.
 +HTTP request sent, awaiting response... 200 OK
 +Length: 154348 (151K) [application/x-gzip]
 +Saving to: “fluent-3ddp-mpi.tar.gz”
 +
 +100%[==================================================================>] 154,348     --.-K/s   in 0.003s  
 +
 +2012-10-01 15:46:12 (48.7 MB/s) - “fluent-3ddp-mpi.tar.gz” saved [154348/154348]
 +
 +</code>
 +<code text>
 +[traine@mills traine]$ tar -zxvf fluent-3ddp-mpi.tar.gz
 +fluent-3ddp-mpi/
 +fluent-3ddp-mpi/3d.cas
 +fluent-3ddp-mpi/input-3d
 +fluent-3ddp-mpi/fluent-3ddp.qs
 +</code>
 +<code text>
 +[traine@mills traine]$ cd fluent-3ddp-mpi
 +</code>
 +<code text>
 +[traine@mills fluent-3ddp-mpi]$ vi fluent-3ddp.qs
 +</code>
 +  * You **must** edit this file to gain access to this licensed product.  Follow the usage directions in the comments.
 +<code text>
 +[traine@mills fluent-3ddp-mpi]$ workgroup -g it_css
 +</code>
 +<code text>
 +[(it_css:traine)@mills fluent-3ddp-mpi]$ qsub fluent-3ddp.qs 
 +Your job 82746 ("fluent-3ddp.qs") has been submitted
 +</code>
 +
 +
 +===== Files =====
 +
 +==== Batch file ====
 +''fluent-3ddp.qs'' file:  (Must supply a port and license server)
 +<code bash>
 +#$ -pe openmpi 4
 +#$ -l  psm_endpoints=1
 +
 +source /opt/shared/valet/docs/valet.sh
 +
 +export ANSYSLMD_LICENSE_FILE=port@ls.udel.edu
 +vpkg_require ansys
 +
 +echo "-- begin fluent run --"
 +fluent 3ddp -g -i input-3d -t$NSLOTS -pinfiniband -mpi=openmpi -ssh
 +echo "-- end fluent run --"
 +</code>
 +
 +==== Input file ====
 +''input-3d'' file:
 +<code text>
 +; Read case file
 +rc 3d.cas
 +; Initialize the solution
 +/solve/init/init
 +; Calculate 50 iterations
 +it 50
 +; Write data file
 +wd it50-3d.dat
 +; Calculate another 50 iterations
 +it 50
 +; Write final data file
 +wd 3d.dat
 +; Exit Fluent
 +exit
 +yes
 +</code>
 +
 +
 +==== Output file ====
 +
 +The fluent output with be in the queue script output file between the "-- begin fluent run --" and "-- end fluent run --" lines.
 +For example:
 +<code text>
 +-- begin fluent run --
 +/opt/shared/ansys/14/v140/fluent/fluent14.0.0/bin/fluent -r14.0.0 3ddp -g -i input-3d -t4 -pinfiniband -mpi=openmpi -ssh
 +/opt/shared/ansys/14/v140/fluent/fluent14.0.0/bin/fluent -r14.0.0 3ddp -g -i input-3d -t4 -pinfiniband -mpi=openmpi -ssh -sgeup
 +/opt/shared/ansys/14/v140/fluent/fluent14.0.0/cortex/lnamd64/cortex.14.0.0 -f fluent -g -i input-3d -newcx (fluent "3ddp -pinfiniband  -host -alnamd64 -r14.0.0 -t4 -mpi=openmpi -cnf=/tmp/fluent-sge-cnf-traine-11579 -path/opt/shared/ansys/14/v140/fluent -sge -ssh")
 +Loading "/opt/shared/ansys/14/v140/fluent/fluent14.0.0/lib/fluent.dmp.114-64"
 +Done.
 +/opt/shared/ansys/14/v140/fluent/fluent14.0.0/bin/fluent -r14.0.0 3ddp -pinfiniband -host -alnamd64 -t4 -mpi=openmpi -cnf=/tmp/fluent-sge-cnf-traine-11579 -path/opt/shared/ansys/14/v140/fluent -sge -ssh -cx n015.mills.hpc.udel.edu:50609:47657
 +/opt/shared/ansys/14/v140/fluent/fluent14.0.0/bin/fluent -r14.0.0 3ddp -pinfiniband -host -alnamd64 -t4 -mpi=openmpi -cnf=/tmp/fluent-sge-cnf-traine-11579 -path/opt/shared/ansys/14/v140/fluent -sge -ssh -cx n015.mills.hpc.udel.edu:50609:47657 -sgeup
 +Starting /opt/shared/ansys/14/v140/fluent/fluent14.0.0/lnamd64/3ddp_host/fluent.14.0.0 sge host -cx n015.mills.hpc.udel.edu:50609:47657 "(list (rpsetvar (QUOTE parallel/function) "fluent 3ddp -flux -node -alnamd64 -r14.0.0 -t4 -pinfiniband -mpi=openmpi -cnf=/tmp/fluent-sge-cnf-traine-12092 -sge -ssh") (rpsetvar (QUOTE parallel/rhost) "") (rpsetvar (QUOTE parallel/ruser) "") (rpsetvar (QUOTE parallel/nprocs_string) "4") (rpsetvar (QUOTE parallel/auto-spawn?) #t) (rpsetvar (QUOTE parallel/trace-level) 0) (rpsetvar (QUOTE parallel/remote-shell) 1) (rpsetvar (QUOTE parallel/path) "/opt/shared/ansys/14/v140/fluent") (rpsetvar (QUOTE parallel/hostsfile) "/tmp/fluent-sge-cnf-traine-12092") )"
 +
 +     Welcome to ANSYS FLUENT 14.0.0
 +
 +     Copyright 2011 ANSYS, Inc.. All Rights Reserved.
 +     Unauthorized use, distribution or duplication is prohibited.
 +     This product is subject to U.S. laws governing export and re-export.
 +     For full Legal Notice, see documentation.
 +
 +Build Time: Oct 25 2011 11:19:48 EDT  Build Id: 10398
 +Loading "/opt/shared/ansys/14/v140/fluent/fluent14.0.0/lib/flprim.dmp.1119-64"
 +Done.
 + 
 +
 +     --------------------------------------------------------------
 +     This is an academic version of ANSYS FLUENT. Usage of this product
 +     license is limited to the terms and conditions specified in your ANSYS
 +     license form, additional terms section.
 +     --------------------------------------------------------------
 +Host spawning Node 0 on machine "n015" (unix).
 +/opt/shared/ansys/14/v140/fluent/fluent14.0.0/bin/fluent -r14.0.0 3ddp -flux -node -alnamd64 -t4 -pinfiniband -mpi=openmpi -cnf=/tmp/fluent-sge-cnf-traine-12092 -sge -ssh -mport 10.54.50.15:10.54.50.15:56389:0
 +/opt/shared/ansys/14/v140/fluent/fluent14.0.0/bin/fluent -r14.0.0 3ddp -flux -node -alnamd64 -t4 -pinfiniband -mpi=openmpi -cnf=/tmp/fluent-sge-cnf-traine-12092 -sge -ssh -mport 10.54.50.15:10.54.50.15:56389:0 -sgeup
 +Starting fixfiledes /opt/shared/ansys/14/v140/fluent/fluent14.0.0/multiport/mpi/lnamd64/openmpi/bin/mpirun --app /tmp/fluent-appfile.12486
 +
 +------------------------------------------------------------------------------
 +ID     Comm.   Hostname        O.S.        PID     Mach ID HW ID   Name        
 +------------------------------------------------------------------------------
 +host   net     n015            Linux-64    12165   0       19      Fluent Host 
 +n3     openmpi n015            Linux-64    12616   0       3       Fluent Node 
 +n2     openmpi n015            Linux-64    12615   0       2       Fluent Node 
 +n1     openmpi n015            Linux-64    12614   0       1       Fluent Node 
 +n0*    openmpi n015            Linux-64    12613   0       0       Fluent Node 
 +
 +Selected system interconnect: InfiniBand
 +------------------------------------------------------------------------------
 +
 +
 +Initializing SGE
 +Done.
 +
 +Reading journal file input...
 +
 +> 
 +Multicore SMT processors detected. Processor affinity set!
 +; Read case file
 +rc 3d.cas
 +
 +Reading "3d.cas"...
 +Using buffering for scanning file.
 +
 +    4000 hexahedral cells, zone  2, binary.
 +    1600 quadrilateral wall faces, zone  3, binary.
 +     100 quadrilateral pressure-outlet faces, zone  4, binary.
 +     100 quadrilateral velocity-inlet faces, zone  5, binary.
 +   11100 quadrilateral interior faces, zone  7, binary.
 +    4961 nodes, binary.
 +    4961 node flags, binary.
 +
 +Building...
 +     mesh
 + auto partitioning mesh by Metis (fast),
 + distributing mesh
 + parts....,
 + faces....,
 + nodes....,
 + cells....,
 +     materials,
 +     interface,
 +     domains,
 + mixture
 +     zones,
 + default-interior
 + velocity_inlet.1
 + pressure_outlet.2
 + wall
 + fluid
 +     parallel,
 +Done.
 +
 +> ; Initialize the solution
 +/solve/init/init
 +
 +> ; Calculate 50 iterations
 +it 50
 +  iter continuity x-velocity y-velocity z-velocity     time/iter
 +     1 1.0000e+00 3.0626e+01 0.0000e+00 0.0000e+00  0:00:01   49
 +     2 5.2224e-01 1.8645e-02 9.7302e-04 9.3701e-04  0:00:01   48
 +     3 3.4389e-01 1.1462e-02 3.6203e-04 3.3080e-04  0:00:01   47
 +     4 2.6015e-01 7.1708e-03 1.8307e-04 1.6784e-04  0:00:02   46
 +     5 1.6257e-01 3.6794e-03 1.1499e-04 1.1104e-04  0:00:02   45
 +     6 1.1773e-01 2.9507e-03 1.0063e-04 9.8831e-05  0:00:01   44
 +     7 8.9668e-02 2.6900e-03 9.9205e-05 9.6483e-05  0:00:01   43
 +     8 7.2522e-02 2.5473e-03 8.9085e-05 8.7391e-05  0:00:01   42
 +     9 5.9407e-02 2.3933e-03 7.3671e-05 7.2378e-05  0:00:01   41
 +    10 4.3260e-02 2.1616e-03 6.6998e-05 6.6789e-05  0:00:01   40
 +    11 3.3065e-02 2.0107e-03 6.3300e-05 6.2885e-05  0:00:01   39
 +  iter continuity x-velocity y-velocity z-velocity     time/iter
 +    12 2.6991e-02 1.8833e-03 5.8103e-05 5.7767e-05  0:00:01   38
 +    13 2.0547e-02 1.7679e-03 5.2381e-05 5.2213e-05  0:00:01   37
 +    14 1.6036e-02 1.6245e-03 4.5816e-05 4.5595e-05  0:00:01   36
 +    15 1.2198e-02 1.4862e-03 4.0081e-05 3.9796e-05  0:00:01   35
 +    16 9.6683e-03 1.3218e-03 3.5188e-05 3.4946e-05  0:00:01   34
 +    17 7.5870e-03 1.1556e-03 3.0637e-05 3.0361e-05  0:00:01   33
 +    18 5.5529e-03 9.9136e-04 2.6857e-05 2.6885e-05  0:00:01   32
 +    19 4.1636e-03 8.3279e-04 2.4361e-05 2.4271e-05  0:00:00   31
 +    20 3.2192e-03 6.8891e-04 2.2513e-05 2.2368e-05  0:00:00   30
 +    21 2.5922e-03 5.5693e-04 2.0894e-05 2.0774e-05  0:00:00   29
 +    22 2.2036e-03 4.4272e-04 1.9067e-05 1.9030e-05  0:00:00   28
 +  iter continuity x-velocity y-velocity z-velocity     time/iter
 +    23 1.8422e-03 3.4535e-04 1.6883e-05 1.6860e-05  0:00:00   27
 +    24 1.5145e-03 2.6291e-04 1.4504e-05 1.4497e-05  0:00:00   26
 +    25 1.2806e-03 1.9693e-04 1.2115e-05 1.2065e-05  0:00:00   25
 +    26 1.0292e-03 1.4402e-04 9.8752e-06 9.8899e-06  0:00:00   24
 +!   27 solution is converged
 +    27 8.3820e-04 1.0405e-04 7.8272e-06 7.8486e-06  0:00:00   23
 +
 +> ; Write data file
 +wd it50-3d.dat
 +
 +Writing "it50-3d.dat"...
 +Done.
 +
 +
 +> ; Calculate another 50 iterations
 +it 50
 +  iter continuity x-velocity y-velocity z-velocity     time/iter
 +!   27 solution is converged
 +    27 8.3820e-04 1.0405e-04 7.8272e-06 7.8486e-06  0:00:01   50
 +!   28 solution is converged
 +    28 6.7773e-04 7.3765e-05 6.0637e-06 6.0806e-06  0:00:01   49
 +
 +> ; Write another data file
 +wd 3d.dat
 +
 +Writing "3d.dat"...
 +Done.
 +
 +
 +> ; Exit Fluent
 +exit
 +The current case has not been saved.
 +OK to discard? [cancel] 
 +yes
 +-- end fluent run --
 +</code>
 +
 +==== Data files ====
 +
 +The files "it50-3d.dat" and "3d.dat" are written and stored in the working directory.  You can load them along with the ''3d.cas'' file for further post-processing and visualization.
 +
 +===== Additional Resources =====
 +  * [[https://www.3ds.com/products-services/simulia/products/abaqus/|ANSYS Fluent]]