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gnikit / gmsh-fpm

Gmsh API using the Fortran Package Manager (fpm)
https://gmsh.info/
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Problem getting the examples to run #8

Closed gareth-nx closed 7 months ago

gareth-nx commented 2 years ago

This is my initial attempt at using gmsh-fpm.

I downloaded the gmsh SDK, and separately cloned the gmsh-fpm source code.

I then compile by running the following from within the gmsh-fpm directory:

export GMSH_SDK_LIB=/home/gareth/LocalInstalls/gmesh/gmesh_sdk/gmsh-git-Linux64-sdk/lib
export LD_LIBRARY_PATH=$GMSH_SDK_LIB:$LD_LIBRARY_PATH
fpm build --link-flag "-L$GMSH_SDK_LIB"

where $GMSH_SDK_LIB is the location of the SDK files. 

gareth@gareth-P410:~/Code_Experiments/fortran/gmsh-fpm/gmsh-fpm$ ls $GMSH_SDK_LIB
gmsh-4.11.0.dev1.dist-info  gmsh.jl  gmsh.py  libgmsh.so  libgmsh.so.4.11  libgmsh.so.4.11.0

These steps seem to work fine (output below).

 + mkdir -p build/dependencies
gmsh.f90                               done.
libgmsh.a                              done.
t13.f90                                done.
t15.f90                                done.
t10.f90                                done.
t9.f90                                 done.
t12.f90                                done.
t18.f90                                done.
t1.f90                                 done.
t16.f90                                done.
t2.f90                                 done.
t5.f90                                 done.
t17.f90                                done.
t20.f90                                done.
t11.f90                                done.
t8.f90                                 done.
t6.f90                                 done.
t7.f90                                 done.
t19.f90                                done.
t14.f90                                done.
t21.f90                                done.
t4.f90                                 done.
t3.f90                                 done.
main.f90                               done.
t13                                    done.
t15                                    done.
t10                                    done.
t9                                     done.
t12                                    done.
t18                                    done.
t1                                     done.
t16                                    done.
t2                                     done.
t5                                     done.
t17                                    done.
t20                                    done.
t11                                    done.
t8                                     done.
t6                                     done.
t7                                     done.
t19                                    done.
t14                                    done.
t21                                    done.
t4                                     done.
t3                                     done.
gmsh                                   done.
[100%] Project compiled successfully.

But then it fails when I try to run an example:

fpm run --example t13 --runner cp -- example/fortran/ && pushd example/fortran/ && ./t13 && rm t13 && popd

with output:

t13                                    failed.
[  4%] Compiling...
/usr/bin/ld: cannot find -lgmsh
collect2: error: ld returned 1 exit status
<ERROR> Compilation failed for object " t13 "
<ERROR>stopping due to failed compilation
STOP 1

I also tried a workaround by adding --link_flag to the command. 

fpm run --link-flag "-L$GMSH_SDK_LIB" --example t13 --runner cp -- example/fortran/ && pushd example/fortran/ && ./t13 && rm t13 && popd

This also failed, but in a different way.

Project is up to date
~/Code_Experiments/fortran/gmsh-fpm/gmsh-fpm/example/fortran ~/Code_Experiments/fortran/gmsh-fpm/gmsh-fpm

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0  0x7fc84d14617d in ???
#1  0x7fc84d14573d in ???
#2  0x7fc8499b108f in ???
#3  0x7fc849af974f in ???
#4  0x55ac20d233ff in istring_
    at ./src/gmsh.f90:14895
#5  0x55ac20d223c7 in ivectorstring_
    at ./src/gmsh.f90:14924
#6  0x55ac20d7fc0e in __gmsh_MOD_gmshinitialize
    at ./src/gmsh.f90:898
#7  0x55ac20d17bbd in t13
    at example/fortran/t13.f90:20
#8  0x55ac20d18580 in main
    at example/fortran/t13.f90:12
Segmentation fault (core dumped)

Any suggestions as to what I'm doing wrong? Thanks!

gnikit commented 2 years ago

Try using --profile release. I noticed this too when compiling with fpm, but I was unable to replicate the problem when I wrote the example tutorials for Gmsh, which I compiled manually. I think fpm is doing something wrong in the background but I haven't found time to look into it.

A bash script build example

#!/bin/bash

GMSH_LIB=../../build     # path to libgmsh.so
FCFLAGS="-g -Wpedantic -Wpedantic -Wno-unused-function -Wno-maybe-uninitialized"
FLINKER="-L${GMSH_LIB} -Wl,-rpath=${GMSH_LIB} -lgmsh"

TEST="t14"
rm -f *.mod *.o *.msh

gfortran $FCFLAGS -o $TEST.o ../../src/gmsh.f90 $TEST.f90 $FLINKER
./$TEST.o
gareth-nx commented 2 years ago

I was able to get it to work by adding --profile release to fpm AND passing the --link-flag option explicitly, like this:

# Path to the "lib" directory in the gmsh sdk
GMSH_SDK_LIB=/home/gareth/LocalInstalls/gmesh/gmesh_sdk/gmsh-git-Linux64-sdk/lib

export LD_LIBRARY_PATH=$GMSH_SDK_LIB:$LD_LIBRARY_PATH

## Works with release build, segfaults with debug build
FPM_PROFILE=release # debug

fpm build --link-flag "-L$GMSH_SDK_LIB" --profile $FPM_PROFILE

fpm run --example t13 --profile $FPM_PROFILE --link-flag "-L$GMSH_SDK_LIB" --runner cp -- example/fortran/ && pushd example/fortran/ && ./t13 && rm t13 && popd

The script is run in the gmsh-fpm top directory. It fails if I use a debug build or if I remove the --link-flag option in the final line.

It might be good to add these flags to the README instructions, at least until the other issues are sorted out?

Just to be clear -- when it works I get a GUI popup with the mesh, and the terminal output below:

 + mkdir -p build/dependencies
gmsh.f90                               done.
libgmsh.a                              done.
t13.f90                                done.
t15.f90                                done.
t10.f90                                done.
t9.f90                                 done.
t12.f90                                done.
t18.f90                                done.
t1.f90                                 done.
t16.f90                                done.
t2.f90                                 done.
t5.f90                                 done.
t17.f90                                done.
t20.f90                                done.
t11.f90                                done.
t8.f90                                 done.
t6.f90                                 done.
t7.f90                                 done.
t19.f90                                done.
t14.f90                                done.
t21.f90                                done.
t4.f90                                 done.
t3.f90                                 done.
main.f90                               done.
t13                                    done.
t15                                    done.
t10                                    done.
t9                                     done.
t12                                    done.
t18                                    done.
t1                                     done.
t16                                    done.
t2                                     done.
t5                                     done.
t17                                    done.
t20                                    done.
t11                                    done.
t8                                     done.
t6                                     done.
t7                                     done.
t19                                    done.
t14                                    done.
t21                                    done.
t4                                     done.
t3                                     done.
gmsh                                   done.
[100%] Project compiled successfully.
Project is up to date
~/Code_Experiments/fortran/gmsh-fpm/gmsh-fpm/example/fortran ~/Code_Experiments/fortran/gmsh-fpm/gmsh-fpm ~/Code_Experiments/fortran/gmsh-fpm/gmsh-fpm ~/Code_Experiments/fortran/gmsh-fpm/gmsh-fpm ~/Code_Experiments/fortran/gmsh-fpm/gmsh-fpm ~/Code_Experiments/fortran/gmsh-fpm/gmsh-fpm ~/Code_Experiments/fortran/gmsh-fpm/gmsh-fpm
Info    : Clearing all models and views...
Info    : Done clearing all models and views
Info    : Reading '../t13_data.stl'...
Info    : 1580 facets in solid 0 Created by Gmsh
Info    : Done reading '../t13_data.stl'
Info    : Classifying surfaces (angle: 40)...
Info    : Found 11 model surfaces
Info    : Found 12 model curves
Info    : Done classifying surfaces (Wall 0.0137293s, CPU 0.070607s)
Info    : Creating geometry of discrete curves...
Info    : Done creating geometry of discrete curves (Wall 9.885e-05s, CPU 0.000509s)
Info    : Creating geometry of discrete surfaces...
Info    : [ 20%] Discrete surface 4 is planar, simplifying parametrization  
Info    : [ 70%] Discrete surface 9 is planar, simplifying parametrization  
Info    : [ 80%] Discrete surface 10 is planar, simplifying parametrization 
Info    : [ 90%] Discrete surface 11 is planar, simplifying parametrization 
Info    : [100%] Discrete surface 12 is planar, simplifying parametrization 
Info    : Done creating geometry of discrete surfaces (Wall 0.0355313s, CPU 0.182178s)
Info    : Meshing 1D...
Info    : [  0%] Meshing curve 14 (Discrete curve)
Info    : [ 10%] Meshing curve 15 (Discrete curve)
Info    : [ 20%] Meshing curve 16 (Discrete curve)
Info    : [ 30%] Meshing curve 17 (Discrete curve)
Info    : [ 40%] Meshing curve 18 (Discrete curve)
Info    : [ 50%] Meshing curve 19 (Discrete curve)
Info    : [ 50%] Meshing curve 20 (Discrete curve)
Info    : [ 60%] Meshing curve 21 (Discrete curve)
Info    : [ 70%] Meshing curve 22 (Discrete curve)
Info    : [ 80%] Meshing curve 23 (Discrete curve)
Info    : [ 90%] Meshing curve 24 (Discrete curve)
Info    : [100%] Meshing curve 25 (Discrete curve)
Info    : Done meshing 1D (Wall 0.00558438s, CPU 0.037403s)
Info    : Meshing 2D...
Info    : [  0%] Meshing surface 2 (Discrete surface, Frontal-Delaunay)
Info    : [ 10%] Meshing surface 3 (Discrete surface, Frontal-Delaunay)
Info    : [ 10%] Triangle not found for first derivative at uv=(-0.442636,0.607606) on discrete surface 3
Info    : [ 10%] Triangle not found for first derivative at uv=(0.26179,-0.757267) on discrete surface 3
Info    : [ 10%] Triangle not found for first derivative at uv=(0.432464,-0.616638) on discrete surface 3
Info    : [ 10%] Triangle not found for first derivative at uv=(-0.563291,0.500538) on discrete surface 3
Info    : [ 10%] Triangle not found for first derivative at uv=(-0.289088,0.735323) on discrete surface 3
Info    : [ 10%] Triangle not found for first derivative at uv=(0.27984,-0.743783) on discrete surface 3
Info    : [ 10%] Triangle not found for first derivative at uv=(0.69775,-0.373345) on discrete surface 3
Info    : [ 10%] Triangle not found for first derivative at uv=(-0.707197,0.364865) on discrete surface 3
Info    : [ 10%] Triangle not found for first derivative at uv=(-0.00138224,0.14449) on discrete surface 3
Info    : [ 10%] Triangle not found for first derivative at uv=(-0.464239,0.588471) on discrete surface 3
Info    : [ 10%] Triangle not found for first derivative at uv=(0.450343,-0.600803) on discrete surface 3
Info    : [ 10%] Triangle not found for first derivative at uv=(-0.544676,0.517092) on discrete surface 3
Info    : [ 10%] Triangle not found for first derivative at uv=(0.530775,-0.529425) on discrete surface 3
Info    : [ 10%] Triangle not found for first derivative at uv=(0.333673,0.0217095) on discrete surface 3
Info    : [ 10%] Triangle not found for first derivative at uv=(0.0869144,0.301251) on discrete surface 3
Info    : [ 10%] Meshing surface 3 (Discrete surface, MeshAdapt)
Info    : [ 10%] Triangle not found for first derivative at uv=(-0.442636,0.607606) on discrete surface 3
Info    : [ 10%] Triangle not found for first derivative at uv=(0.26179,-0.757267) on discrete surface 3
Info    : [ 10%] Triangle not found for first derivative at uv=(0.432464,-0.616638) on discrete surface 3
Info    : [ 10%] Triangle not found for first derivative at uv=(-0.563291,0.500538) on discrete surface 3
Info    : [ 20%] Meshing surface 4 (Discrete surface, Frontal-Delaunay)
Info    : [ 30%] Meshing surface 5 (Discrete surface, Frontal-Delaunay)
Info    : [ 30%] Triangle not found for first derivative at uv=(-0.714411,-0.642864) on discrete surface 5
Info    : [ 30%] Triangle not found for first derivative at uv=(0.714411,0.642864) on discrete surface 5
Info    : [ 40%] Meshing surface 6 (Discrete surface, Frontal-Delaunay)
Info    : [ 50%] Meshing surface 7 (Discrete surface, Frontal-Delaunay)
Info    : [ 60%] Meshing surface 8 (Discrete surface, Frontal-Delaunay)
Info    : [ 70%] Meshing surface 9 (Discrete surface, Frontal-Delaunay)
Info    : [ 80%] Meshing surface 10 (Discrete surface, Frontal-Delaunay)
Info    : [ 90%] Meshing surface 11 (Discrete surface, Frontal-Delaunay)
Info    : [100%] Meshing surface 12 (Discrete surface, Frontal-Delaunay)
Info    : Done meshing 2D (Wall 0.46171s, CPU 0.466386s)
Info    : Meshing 3D...
Info    : 3D Meshing 1 volume with 1 connected component
Info    : Tetrahedrizing 3823 nodes...
Info    : Done tetrahedrizing 3831 nodes (Wall 0.0396563s, CPU 0.039654s)
Info    : Reconstructing mesh...
Info    :  - Creating surface mesh
Info    :  - Identifying boundary edges
Info    :  - Recovering boundary
Info    : Done reconstructing mesh (Wall 0.0813547s, CPU 0.078091s)
Warning : No tetrahedra in region 1
Info    : 3D refinement terminated (4222 nodes total):
Info    :  - 0 Delaunay cavities modified for star shapeness
Info    :  - 0 nodes could not be inserted
Info    :  - 0 tetrahedra created in 2.5638e-05 sec. (0 tets/s)
Error   : No elements in volume 1 
Info    : Writing 't13.msh'...
Info    : Done writing 't13.msh'
-------------------------------------------------------
Version       : 4.11.0-git-32bdc2514
License       : GNU General Public License
Build OS      : Linux64-sdk
Build date    : 20220908
Build host    : gmsh.info
Build options : 64Bit ALGLIB[contrib] ANN[contrib] Bamg Blas[petsc] Blossom Cgns DIntegration Dlopen DomHex Eigen[contrib] Fltk Gmm[contrib] Hxt Jpeg Kbipack Lapack[petsc] LinuxJoystick MathEx[contrib] Med Mesh Metis[contrib] Mmg Mpeg Netgen ONELAB ONELABMetamodel OpenCASCADE OpenCASCADE-CAF OpenGL OpenMP OptHom PETSc Parser Plugins Png Post QuadMeshingTools QuadTri Solver TetGen/BR Voro++[contrib] WinslowUntangler Zlib
FLTK version  : 1.4.0
PETSc version : 3.14.4 (real arithmtic)
OCC version   : 7.6.1
MED version   : 4.1.0
Packaged by   : geuzaine
Web site      : https://gmsh.info
Issue tracker : https://gitlab.onelab.info/gmsh/gmsh/issues
-------------------------------------------------------

Thanks for your help.

gnikit commented 7 months ago

This is now fixed and a continuous integration workflow of the Fortran examples with the latest Gmsh SDK has been added on GitHub.