Sculpt not running on basic example

Coreform Cubit
#1

Coreform Cubit Version: 2023.11
Platform: Ubuntu 23.10
Hello,
Issue
I am not able to mesh with sculpt the simple example which is provided in the documentation
sphere rad 1
sphere rad 1
vol 2 mov x 2
cylinder rad 1 height 2
vol 3 rota 90 about y
vol 3 mov x 1
unite vol all
sculpt parallel
It gives:
Cubit>sculpt parallel

ERROR: Invalid Command: sculpt parallel
and the path is:
sculpt parallel path list
Cubit>sculpt parallel path list
Sculpt paths:
sculpt = /opt/Coreform-Cubit-2023.11/bin/sculpt
epu = /opt/Coreform-Cubit-2023.11/bin/epu
mpiexec = mpiexec
Finished Command: sculpt parallel path list
It seems that I am not using the mpiexec of cubit.
Is it the problem ? and how can I fix it ?
Thanks,
Paul

#2

hi @paul,

sculpt parallel

is an incomplete command. That’s why cubit throws the error here. you need to at least tell sculpt what you want to mesh

sculpt volume all 
# or
#sculpt parallel volume all

grafik
grafik1012×864 47 KB

#3

Thanks a lot! I just follow the documentation…
I tried to generate a mesh using the suggested command but got an error from mpiexec.
Initializing MPI on 16 Processors: mpiexec = /usr/bin/mpiexec

/usr/bin/mpiexec -n 16 /opt/Coreform-Cubit-2023.11/bin/psculpt -j 16 -x 36 -y 20 -z 20 -t -1.349116 -u -1.305064 -v -1.305064 -q 3.349116 -r 1.305064 -s 1.305064 -e sculpt_parallel.diatom_result -d sculpt_parallel.diatom

/usr/bin/mpiexec: Error: unknown option “-n”

ERROR: Sculpt Aborted. No mesh was generated. Check log file for details

Sculpt log file written: sculpt_parallel.log

ERROR: Command Failed.
As I expected the mpiexec I have (version from openmpi 4.1.5) is not working. I checked and realized that the one from cubit corresponds to an openmpi version of 4.1.4. In between, the option -n is no longer supported and one should use -np only.
I change the path to mpiexec:
sculpt parallel path mpiexec “/opt/Coreform-Cubit-2023.11/bin/mpiexec”
but unfortunately it didn’t work. I got the following error message:
There are not enough slots available in the system to satisfy the 16
slots that were requested by the application:

/opt/Coreform-Cubit-2023.11/bin/psculpt

Either request fewer slots for your application, or make more slots
available for use.
I need to add the --oversubscribe option or be able to control the number of threads. I tried to add the option to the path to mpiexec but it didn’t work.
How can I solve this problem?
Thanks,
Paul

#4

Can you try running with 1 processor again

sculpt volume all processors 1 no_clean

Could you also please share the content of your sculpt_parallel.log and sculpt_parallel.bat

#5

It worked!
Thanks a lot. Does it mean that I have to change 1 to another value to run in parallel?
Here is the content of sculpt_parallel.log
SCULPT Running on host name: cristini-Precision-7560
At time: Mon Feb 26 12:28:51 2024

Initializing MPI on 1 Processors: mpiexec = /opt/Coreform-Cubit-2023.11/bin/mpiexec

/opt/Coreform-Cubit-2023.11/bin/mpiexec -n 1 /opt/Coreform-Cubit-2023.11/bin/psculpt -j 1 -x 36 -y 20 -z 20 -t -1.349116 -u -1.305064 -v -1.305064 -q 3.349116 -r 1.305064 -s 1.305064 -e sculpt_parallel.diatom_result -d sculpt_parallel.diatom
[2024-02-26 12:28:52.428] [e[32minfoe[m] RLM session initialized
QObject::startTimer: Timers can only be used with threads started with QThread
QObject::startTimer: Timers can only be used with threads started with QThread
QObject::startTimer: Timers can only be used with threads started with QThread
QObject::startTimer: Timers can only be used with threads started with QThread
QObject::startTimer: Timers can only be used with threads started with QThread
SANDIA NATIONAL LABORATORIES

 SSSSS     CCCCC    UU   UU   LL        PPPPPP    TTTTTT
SS   SS   CC   CC   UU   UU   LL        PP   PP     TT
SS        CC        UU   UU   LL        PP   PP     TT
 SSSSS    CC        UU   UU   LL        PPPPPP      TT
     SS   CC        UU   UU   LL        PP          TT
SS   SS   CC   CC   UU   UU   LL        PP          TT
 SSSSS     CCCCC     UUUUU    LLLLLLL   PP          TT

                 PARALLEL HEX MESHING
                        FROM
                 VOLUME FRACTION DATA

          SCULPT Version 16.12.6 Build b14f6c8f
          Copyright 2015 Sandia Corporation
  Revised Thu Nov 2 20:37:30 2023 +0000
  User Support and Bug Reports: cubit-help@sandia.gov

 SCULPT includes CAMAL by Sandia National Laboratories

SCULPT includes CTH Diatoms by Sandia National Laboratories
SCULPT is a companion application to the CUBIT Geometry and
Meshing Toolkit by Sandia National Laboratories

Input: /opt/Coreform-Cubit-2023.11/bin/psculpt
–num_procs -j 1
–diatom_file -d sculpt_parallel.diatom
–exodus_file -e sculpt_parallel.diatom_result
–nelx -x 36
–nely -y 20
–nelz -z 20
–xmin -t -1.349116
–ymin -u -1.305064
–zmin -v -1.305064
–xmax -q 3.349116
–ymax -r 1.305064
–zmax -s 1.305064

Total Cells = 14400
Number of Processors = 1
Approx. Num Cells per Proc = 14400

Decomposing Cartesian grid for parallel…
Rank 0 Number of cells/segment in directions X 36
Rank 0 Number of cells/segment in directions Y 20
Rank 0 Number of cells/segment in directions Z 20
Global Number of grid segments in directions X 1
Global Number of grid segments in directions Y 1
Global Number of grid segments in directions Z 1

initializing geometry…
Parsing diatom input
Finished loading diatom master buffer
Finished creating diatoms

STL summary: fn=sculpt_parallel_Volume_1.stl vertices=8838 Triangles=2946
Bounding box:
xmin=-1.000000 xmax=2.998103
ymin=-1.000000 ymax=1.000000
zmin=-1.000000 zmax=1.000000
Side length min=0.003712 length max=2.003784
angle min=0.135741 angle max=161.913832 degrees
area min=1.746067e-05 area max=0.123091
Checking Triangle Side Matches Triangle Id=0
Diatom STL All Sides Properly matched

inserting volume fractions…
begin SCULPT meshing…
(1/9) computing normals…
(2/9) classifying materials…
(3/9) resolving non-manifolds…
(4/9) computing dual edge intersections…
(5/9) computing material interfaces…
(6/9) generating geometry…
(7/9) generating buffer hexes…
(8/9) generating interior hexes…
(9/9) begin smoothing…
Begin smoothing hexes using:
Curve Smoothing = SMOOTH_CURV_VFRAC
Surface Smoothing = SMOOTH_SURF_HYBRID
Volume Smoothing = SMOOTH_VOL_HYBRID_CAMAL
Boundary Buffer Improvement = YES
Surface Projection Type = LINEAR_SURFACE_PROJECTION
Laplacian Iterations = 2
Maximum Optimization Iters = 5
Optimization Threshold = 0.600000
Curve Opt. Threshold = 0.100000
Max Parallel Coloring Iters = 100
Parallel Coloring Threshold = 0.200000
Max Guaranteed Quality Iters = 0
Guaranteed Quality Threshold = 0.200000
Laplacian Iter: 1
Laplacian Iter: 2
Smoothing 6832 hexes on 1 processors
Jacobi Opt Iter: 1, Num bad: 0, Num poor: 0, Min SJ: 0.283456
Jacobi Opt Iter: 2, Num bad: 0, Num poor: 0, Min SJ: 0.325482
Jacobi Opt Iter: 3, Num bad: 0, Num poor: 0, Min SJ: 0.326913
Jacobi Opt Iter: 4, Num bad: 0, Num poor: 0, Min SJ: 0.340501
Jacobi Opt Iter: 5, Num bad: 0, Num poor: 0, Min SJ: 0.338385
Begin parallel color smoothing 0 nodes below threshold 0.200000
No parallel color smoothing performed: min SJ > 0.200000
Begin parallel color smoothing 0 nodes below threshold 0.200000
No parallel color smoothing performed: min SJ > 0.200000
building exodus mesh…
generating global ids…
================ MESH SUMMARY ===================
Base Filename sculpt_parallel.diatom_result
Num Procs 1
Num Nodes 7941
Num Elements 6832
Num Blocks 1
Num Nodesets 0
Num Sidesets 0
Num Bad Qual 0
Num Poor Qual 0
Min Quality 0.399690
Avg Quality 0.907877
Min Edge Len 0.060411
Min Qual Rank 0

Job Completed Mon Feb 26 12:28:56 2024

Elapsed Time 1.895089 sec. (0.031585 min.)
Total Time on 1 Procs 1.895089 sec. (0.031585 min.)
Slow Rank 0
Done!

#6

Yes!

The easiest way to try out the sculpt options is to use the sculpt panel in the gui.

image
image362×918 74.2 KB