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October 13, 2015, 16:04 |
Running UDF with Supercomputer
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#1 |
Member
Rui
Join Date: Apr 2015
Location: Montreal. CA
Posts: 49
Rep Power: 11 |
Hello everyone,
I can run UDF on my own computer. Interpret the c.file, set the boundary condition and initialize. However, when I tried to use supercomputer I don't know how to let him understand I'm using UDF. Do I need to compile? Do I need to hook the function? In my trial, I compiled, I built the library. I upload the library folder(called"libudf"), udfconfig.h (headfile),velocity_profile.c(cfile), dat file, cas file, Jou file and job file to the supercomputer Here is my journal file parallel/partition/auto/use-case-file-method yes file/rcd FFF-2.dat.gz file/rcd FFF-2.cas.gz /define/user-defined/compiled-functions compile yes libudf velocity_profile.c file/confirm-overwrite no solve/set/time-step 0.005 solve/set/reportin-interval 100 solve/dual-time-iterate 1000 120 file/write-data FFF-2_1100.dat.gz /exit Here is the output.dat Building... mesh auto partitioning mesh by Metis (fast), distributing mesh parts............................................. ..., faces............................................. ..., nodes............................................. ..., cells............................................. ..., inter-node communication reduction using architecture-aware remapping: 63% materials, interface, domains, mixture zones, outlet bottom_wall side_wall water_surface symmetry inlet interior-fluid fluid parallel, Note: 3d, double precision, pressure-based, large eddy simulation, transient case read into 3d, pressure-based, large eddy simulation, transient solver. Done. Reading ""| gunzip -c \"FFF-2.dat.gz\"""... Parallel variables... Error: chip-exec: function "inlet_z_velocity" not found. Error: chip-exec: function "inlet_z_velocity" not found. Error: chip-exec: function "inlet_z_velocity" not found. Error: chip-exec: function "inlet_z_velocity" not found. Error: chip-exec: function "inlet_z_velocity" not found. Error: chip-exec: function "inlet_z_velocity" not found. Error: chip-exec: function "inlet_z_velocity" not found. Error: chip-exec: function "inlet_z_velocity" not found. Error: chip-exec: function "inlet_z_velocity" not found. Error: chip-exec: function "inlet_z_velocity" not found. Error: chip-exec: function "inlet_z_velocity" not found. Error: chip-exec: function "inlet_z_velocity" not found. Error: chip-exec: function "inlet_z_velocity" not found. Error: chip-exec: function "inlet_z_velocity" not found. Error: chip-exec: function "inlet_z_velocity" not found. Error: chip-exec: function "inlet_z_velocity" not found. Error: chip-exec: function "inlet_z_velocity" not found. Error: chip-exec: function "inlet_z_velocity" not found. Error: chip-exec: function "inlet_z_velocity" not found. Error: chip-exec: function "inlet_z_velocity" not found. Error: chip-exec: function "inlet_z_velocity" not found. Error: chip-exec: function "inlet_z_velocity" not found. Error: chip-exec: function "inlet_z_velocity" not found. Error: chip-exec: function "inlet_z_velocity" not found. Error: chip-exec: function "inlet_z_velocity" not found. Error: chip-exec: function "inlet_z_velocity" not found. Error: chip-exec: function "inlet_z_velocity" not found. Error: chip-exec: function "inlet_z_velocity" not found. Error: chip-exec: function "inlet_z_velocity" not found. Error: chip-exec: function "inlet_z_velocity" not found. Error: chip-exec: function "inlet_z_velocity" not found. Error: chip-exec: function "inlet_z_velocity" not found. Error: chip-exec: function "inlet_z_velocity" not found. Error: chip-exec: function "inlet_z_velocity" not found. Error: chip-exec: function "inlet_z_velocity" not found. Error: chip-exec: function "inlet_z_velocity" not found. Error: chip-exec: function "inlet_z_velocity" not found. Error: chip-exec: function "inlet_z_velocity" not found. Error: chip-exec: function "inlet_z_velocity" not found. Error: chip-exec: function "inlet_z_velocity" not found. Error: chip-exec: function "inlet_z_velocity" not found. Error: chip-exec: function "inlet_z_velocity" not found. Error: chip-exec: function "inlet_z_velocity" not found. Error: chip-exec: function "inlet_z_velocity" not found. Error: chip-exec: function "inlet_z_velocity" not found. Error: chip-exec: function "inlet_z_velocity" not found. Error: chip-exec: function "inlet_z_velocity" not found. Error: chip-exec: function "inlet_z_velocity" not found. Done. Warning: An error or interrupt occurred while reading the journal file. Some commands may not have been completed. > Halting due to end of file on input. So what should I do now? I'll try to hook the function at "initialize" option I'll try to change the command in the journal. Thank you for the help! |
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October 13, 2015, 16:20 |
Another trial
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#2 |
Member
Rui
Join Date: Apr 2015
Location: Montreal. CA
Posts: 49
Rep Power: 11 |
Try another order of the compile. Failed again
Journal: /define/user-defined/compiled-functions compile yes libudf velocity_profile.c parallel/partition/auto/use-case-file-method yes file/rcd FFF-2.dat.gz file/rcd FFF-2.cas.gz file/confirm-overwrite no solve/set/time-step 0.005 solve/set/reportin-interval 100 solve/dual-time-iterate 1000 120 file/write-data FFF-2_1100.dat.gz /exit OUTPUT Host spawning Node 0 on machine "node-e3-80" (unix). /home/apps/Logiciels/ANSYS_CONC/v150/fluent/fluent15.0.0/bin/fluent -r15.0.0 3d -flux -node -t48 -pinfiniband -mpi=pcmpi -cnf=/var/spool/pbs/aux//4076870.egeon2 -ssh -mport 172.20.111.80:172.20.111.80:46427:0 Starting /home/apps/Logiciels/ANSYS_CONC/v150/fluent/fluent15.0.0/multiport/mpi/lnamd64/pcmpi/bin/mpirun -e MPI_USE_MALLOPT_MMAP_MAX=0 -prot -IBV -e MPI_HASIC_IBV=1 -f /tmp/fluent-appfile.30811 Warning: Permanently added '172.20.112.53' (RSA) to the list of known hosts. Warning: Permanently added '172.20.112.56' (RSA) to the list of known hosts. Warning: Permanently added '172.20.112.54' (RSA) to the list of known hosts. IBM Platform MPI licensed for FLUENT. Host 0 -- ip 172.20.111.80 -- ranks 0 - 11 Host 1 -- ip 172.20.112.53 -- ranks 12 - 23 Host 2 -- ip 172.20.112.54 -- ranks 24 - 35 Host 3 -- ip 172.20.112.56 -- ranks 36 - 47 host | 0 1 2 3 ======|===================== 0 : SHM IBV IBV IBV 1 : IBV SHM IBV IBV 2 : IBV IBV SHM IBV 3 : IBV IBV IBV SHM Prot - All Intra-node communication is: SHM Prot - All Inter-node communication is: IBV ------------------------------------------------------------------------------------ ID Comm. Hostname O.S. PID Mach ID HW ID Name ------------------------------------------------------------------------------------ n47 pcmpi node-e4-56 Linux-64 19085 3 47 Fluent Node n46 pcmpi node-e4-56 Linux-64 19084 3 46 Fluent Node n45 pcmpi node-e4-56 Linux-64 19083 3 45 Fluent Node n44 pcmpi node-e4-56 Linux-64 19082 3 44 Fluent Node n43 pcmpi node-e4-56 Linux-64 19081 3 43 Fluent Node n42 pcmpi node-e4-56 Linux-64 19080 3 42 Fluent Node n41 pcmpi node-e4-56 Linux-64 19079 3 41 Fluent Node n40 pcmpi node-e4-56 Linux-64 19078 3 40 Fluent Node n39 pcmpi node-e4-56 Linux-64 19077 3 39 Fluent Node n38 pcmpi node-e4-56 Linux-64 19076 3 38 Fluent Node n37 pcmpi node-e4-56 Linux-64 19075 3 37 Fluent Node n36 pcmpi node-e4-56 Linux-64 19074 3 36 Fluent Node n35 pcmpi node-e4-54 Linux-64 1430 2 35 Fluent Node n34 pcmpi node-e4-54 Linux-64 1429 2 34 Fluent Node n33 pcmpi node-e4-54 Linux-64 1428 2 33 Fluent Node n32 pcmpi node-e4-54 Linux-64 1427 2 32 Fluent Node n31 pcmpi node-e4-54 Linux-64 1426 2 31 Fluent Node n30 pcmpi node-e4-54 Linux-64 1425 2 30 Fluent Node n29 pcmpi node-e4-54 Linux-64 1424 2 29 Fluent Node n28 pcmpi node-e4-54 Linux-64 1423 2 28 Fluent Node ------------------------------------------------------------------------------------ ID Comm. Hostname O.S. PID Mach ID HW ID Name ------------------------------------------------------------------------------------ n27 pcmpi node-e4-54 Linux-64 1422 2 27 Fluent Node n26 pcmpi node-e4-54 Linux-64 1421 2 26 Fluent Node n25 pcmpi node-e4-54 Linux-64 1420 2 25 Fluent Node n24 pcmpi node-e4-54 Linux-64 1419 2 24 Fluent Node n23 pcmpi node-e4-53 Linux-64 25072 1 23 Fluent Node n22 pcmpi node-e4-53 Linux-64 25071 1 22 Fluent Node n21 pcmpi node-e4-53 Linux-64 25070 1 21 Fluent Node n20 pcmpi node-e4-53 Linux-64 25069 1 20 Fluent Node n19 pcmpi node-e4-53 Linux-64 25068 1 19 Fluent Node n18 pcmpi node-e4-53 Linux-64 25067 1 18 Fluent Node n17 pcmpi node-e4-53 Linux-64 25066 1 17 Fluent Node n16 pcmpi node-e4-53 Linux-64 25065 1 16 Fluent Node n15 pcmpi node-e4-53 Linux-64 25064 1 15 Fluent Node n14 pcmpi node-e4-53 Linux-64 25063 1 14 Fluent Node n13 pcmpi node-e4-53 Linux-64 25062 1 13 Fluent Node n12 pcmpi node-e4-53 Linux-64 25061 1 12 Fluent Node host net node-e3-80 Linux-64 30661 0 7 Fluent Host n11 pcmpi node-e3-80 Linux-64 31809 0 11 Fluent Node n10 pcmpi node-e3-80 Linux-64 31808 0 10 Fluent Node n9 pcmpi node-e3-80 Linux-64 31807 0 9 Fluent Node ------------------------------------------------------------------------------------ ID Comm. Hostname O.S. PID Mach ID HW ID Name ------------------------------------------------------------------------------------ n8 pcmpi node-e3-80 Linux-64 31806 0 8 Fluent Node n7 pcmpi node-e3-80 Linux-64 31805 0 7 Fluent Node n6 pcmpi node-e3-80 Linux-64 31804 0 6 Fluent Node n5 pcmpi node-e3-80 Linux-64 31803 0 5 Fluent Node n4 pcmpi node-e3-80 Linux-64 31802 0 4 Fluent Node n3 pcmpi node-e3-80 Linux-64 31801 0 3 Fluent Node n2 pcmpi node-e3-80 Linux-64 31800 0 2 Fluent Node n1 pcmpi node-e3-80 Linux-64 31799 0 1 Fluent Node n0* pcmpi node-e3-80 Linux-64 31798 0 0 Fluent Node Selected system interconnect: InfiniBand ------------------------------------------------------------------------------------ Reading journal file /RQexec/roi247/trial1013z/fluent.jou... > /define/user-defined/compiled-functions compile yes Make sure that UDF source files are in the directory that contains your case and data files. If you have an existing yes directory, please remove this directory to ensure that latest files are used. Continue? [yes] libudf Please answer y[es] or n[o]. Make sure that UDF source files are in the directory that contains your case and data files. If you have an existing yes directory, please remove this directory to ensure that latest files are used. Continue? [yes] velocity_profile.c Please answer y[es] or n[o]. Make sure that UDF source files are in the directory that contains your case and data files. If you have an existing yes directory, please remove this directory to ensure that latest files are used. Continue? [yes] Give C-Source file names: First file name: [""] parallel/partition/auto/use-case-file-method yes Next file name: [""] file/rcd FFF-2.dat.gz Next file name: [""] file/rcd FFF-2.cas.gz Next file name: [""] Give header file names: First file name: [""] file/confirm-overwrite no Next file name: [""] solve/set/time-step 0.005 Next file name: [""] solve/set/reportin-interval 100 Next file name: [""] solve/dual-time-iterate 1000 120 Next file name: [""] file/write-data FFF-2_1100.dat.gz Next file name: [""] Copied ./FFF-2.cas.gz to yes/src Copied ./FFF-2.dat.gz to yes/src "/rcd" is not found Copied file/rcd to yes/src "/rcd" is not found Copied file/rcd to yes/src "/use-case-file-method" is not found Copied parallel/partition/auto/use-case-file-method to yes/src Copied ./yes to yes/src "/0.005" is not found Copied 0.005 to yes/src "/100" is not found Copied 100 to yes/src "/1000" is not found Copied 1000 to yes/src "/120" is not found Copied 120 to yes/src "/FFF-2_1100.dat.gz" is not found Copied FFF-2_1100.dat.gz to yes/src "/confirm-overwrite" is not found Copied file/confirm-overwrite to yes/src "/write-data" is not found Copied file/write-data to yes/src "/no" is not found Copied no to yes/src "/dual-time-iterate" is not found Copied solve/dual-time-iterate to yes/src "/reportin-interval" is not found Copied solve/set/reportin-interval to yes/src "/time-step" is not found Copied solve/set/time-step to yes/src Creating user.udf file for 3d_host ... Creating user.udf file for 3d_node ... Working... for d in lnamd64/[23]*; do \ ( \ cd $d; \ for f in ../../src/*.[ch] ../../src/makefile; do \ if [ ! -f `basename $f` ]; then \ echo "# linking to" $f "in" $d; \ ln -s $f .; \ fi; \ done; \ echo ""; \ echo "# building library in" $d; \ if [ "" = "1" ]; then \ echo "# using gcc64"; \ make ARCHC=gcc64 -k>makelog 2>&1; \ else \ if [ "" = "1" ]; then \ echo "# using gcc"; \ make ARCHC=gcc -k>makelog 2>&1; \ else \ make -k>makelog 2>&1; \ fi; \ fi;\ cat makelog; \ ) \ done # linking to ../../src/*.[ch] in lnamd64/3d_host # building library in lnamd64/3d_host make[1]: Entering directory `/exec5/GROUP/roi247/roi247/trial1013z/yes/lnamd64/3d_host' make[1]: *** No rule to make target `0.005', needed by `FFF-2.cas.gz'. make[1]: *** No rule to make target `100', needed by `FFF-2.cas.gz'. make[1]: *** No rule to make target `1000', needed by `FFF-2.cas.gz'. make[1]: *** No rule to make target `120', needed by `FFF-2.cas.gz'. make[1]: *** No rule to make target `FFF-2_1100.dat.gz', needed by `FFF-2.cas.gz'. make[1]: *** No rule to make target `confirm-overwrite', needed by `FFF-2.cas.gz'. make[1]: *** No rule to make target `write-data', needed by `FFF-2.cas.gz'. make[1]: *** No rule to make target `no', needed by `FFF-2.cas.gz'. make[1]: *** No rule to make target `dual-time-iterate', needed by `FFF-2.cas.gz'. make[1]: *** No rule to make target `reportin-interval', needed by `FFF-2.cas.gz'. make[1]: *** No rule to make target `time-step', needed by `FFF-2.cas.gz'. make[1]: Target `default' not remade because of errors. make[1]: Leaving directory `/exec5/GROUP/roi247/roi247/trial1013z/yes/lnamd64/3d_host' # linking to ../../src/*.[ch] in lnamd64/3d_node # building library in lnamd64/3d_node make[1]: Entering directory `/exec5/GROUP/roi247/roi247/trial1013z/yes/lnamd64/3d_node' make[1]: *** No rule to make target `0.005', needed by `FFF-2.cas.gz'. make[1]: *** No rule to make target `100', needed by `FFF-2.cas.gz'. make[1]: *** No rule to make target `1000', needed by `FFF-2.cas.gz'. make[1]: *** No rule to make target `120', needed by `FFF-2.cas.gz'. make[1]: *** No rule to make target `FFF-2_1100.dat.gz', needed by `FFF-2.cas.gz'. make[1]: *** No rule to make target `confirm-overwrite', needed by `FFF-2.cas.gz'. make[1]: *** No rule to make target `write-data', needed by `FFF-2.cas.gz'. make[1]: *** No rule to make target `no', needed by `FFF-2.cas.gz'. make[1]: *** No rule to make target `dual-time-iterate', needed by `FFF-2.cas.gz'. make[1]: *** No rule to make target `reportin-interval', needed by `FFF-2.cas.gz'. make[1]: *** No rule to make target `time-step', needed by `FFF-2.cas.gz'. make[1]: Target `default' not remade because of errors. make[1]: Leaving directory `/exec5/GROUP/roi247/roi247/trial1013z/yes/lnamd64/3d_node' You can also see the 'log'-file in the working directory for this compilation history Done. > adapt/ mesh/ surface/ define/ parallel/ switch-to-meshing-mode display/ plot/ views/ exit report/ file/ solve/ > adapt/ mesh/ surface/ define/ parallel/ switch-to-meshing-mode display/ plot/ views/ exit report/ file/ solve/ > /exit |
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October 13, 2015, 16:28 |
New trial
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#3 |
Member
Rui
Join Date: Apr 2015
Location: Montreal. CA
Posts: 49
Rep Power: 11 |
I'm Trying to use this one now
/define/user-defined/compiled-functions compile yes velocity_profile.c udfconfig.h parallel/partition/auto/use-case-file-method yes file/rcd FFF-2.dat.gz file/rcd FFF-2.cas.gz file/confirm-overwrite no solve/set/time-step 0.005 solve/set/reportin-interval 100 solve/dual-time-iterate 1000 120 file/write-data FFF-2_1100.dat.gz /exit |
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October 14, 2015, 17:25 |
Still waiting in the super computer
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#4 |
Member
Rui
Join Date: Apr 2015
Location: Montreal. CA
Posts: 49
Rep Power: 11 |
Maybe I should try with a small mesh
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October 15, 2015, 14:41 |
interpret command needed
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#5 |
Member
Rui
Join Date: Apr 2015
Location: Montreal. CA
Posts: 49
Rep Power: 11 |
/define/user-defined/interpreted-functions velocity_profile.c cpp 10000 no
This command doesn't work RESULTS Reading journal file /RQexec/roi247/trial10147/fluent.jou... > /define/user-defined/interpreted-functions velocity_profile.c cpp 10000 Invalid string. no Invalid string. CPP Command Name ["cpp"] /file/read-case Invalid string. file/rcd Invalid string. FFF-2.cas.gz Invalid string. CPP Command Name ["cpp"] /solve/initialize/initialize-flow Invalid string. CPP Command Name ["cpp"] solve/set/time-step Invalid string. 1 Invalid string. CPP Command Name ["cpp"] solve/set/reportin-interval Invalid string. 1 Invalid string. CPP Command Name ["cpp"] solve/dual-time-iterate Invalid string. 10 Invalid string. 10 Invalid string. CPP Command Name ["cpp"] file/write-data Invalid string. FFF-2_1100.dat.gz Invalid string. CPP Command Name ["cpp"] /exit Invalid string. CPP Command Name ["cpp"] yes Invalid string. CPP Command Name ["cpp"] virtual machine stack size [10000] display assembly code listing? [no] Warning: An error or interrupt occurred while reading the journal file. Some commands may not have been completed. > Halting due to end of file on input. |
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