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Old   October 13, 2015, 15:04
Default Running UDF with Supercomputer
  #1
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Rui Zeng
Join Date: Apr 2015
Location: Montreal. CA
Posts: 26
Rep Power: 4
roi247 is on a distinguished road
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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Old   October 13, 2015, 15:20
Default Another trial
  #2
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Rui Zeng
Join Date: Apr 2015
Location: Montreal. CA
Posts: 26
Rep Power: 4
roi247 is on a distinguished road
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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Old   October 13, 2015, 15:28
Default New trial
  #3
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Rui Zeng
Join Date: Apr 2015
Location: Montreal. CA
Posts: 26
Rep Power: 4
roi247 is on a distinguished road
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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Old   October 14, 2015, 16:25
Default Still waiting in the super computer
  #4
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Rui Zeng
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Location: Montreal. CA
Posts: 26
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Maybe I should try with a small mesh
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Old   October 15, 2015, 13:41
Default interpret command needed
  #5
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Rui Zeng
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/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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