View Issue Details
| ID | Project | Category | View Status | Date Submitted | Last Update |
|---|---|---|---|---|---|
| 0003301 | OpenFOAM | Bug | public | 2019-07-02 08:29 | 2020-01-07 11:28 |
| Reporter | paulmedwards | Assigned To | henry | ||
| Priority | normal | Severity | trivial | Reproducibility | always |
| Status | resolved | Resolution | reopened | ||
| Product Version | dev | ||||
| Summary | 0003301: Issue compiling in a path containing a symlink | ||||
| Description | The `/etc/bashrc` will take the physical path for `FOAM_INST_DIR` here: https://github.com/OpenFOAM/OpenFOAM-dev/blob/master/etc/bashrc#L46. This is then used for other environment variables, e.g. WM_PROJECT_INST_DIR and WM_PROJECT_DIR. In the wmake command it compares the current working directory with `WM_PROJECT_DIR` here: https://github.com/edwardsp/OpenFOAM-dev/blob/master/wmake/wmake#L398. Since just `$PWD`is used this will not match if there are symlinks in the path. A possible solution is to change directory to `pwd -P`. | ||||
| Tags | No tags attached. | ||||
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It is not clear how to reproduce this problem, we compile OpenFOAM on many systems with different compilers and operating systems and have not had any such problems. Are you sure your proposed change will work on all systems? How much testing have you performed? |
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In wclean we have expandPath "$PWD" if [ "$exPath" = "$WM_PROJECT_DIR" ] because apparently `pwd -P` does not resolve all potential problems: expandPath() { if [ -d "$1" ] then exPath=$(cd "$1" && pwd -P) else exPath=$(cd $(dirname "$1") && pwd -P) fi } we could use this in wmake also. |
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I haven't done extensive testing here. I have created a script to automate building OpenFOAM and the fix I have is to just switch to the physical path before sourcing bashrc and building: `cd $(readlink -f $BUILD_DIR)`. It was a problem for me as my cluster setup had a frontend as the NFS server. The cluster nodes mount in a different place to where the device is mounted and so symlinks are created on the frontend to keep consistent paths. If WM_INST_DIR is set explicitly to the path with symlinks I would expect it to work (i.e. bashrc#L46 was changed to `export FOAM_INST_DIR=/path/with/symlink`). It is the detection that takes the physical path but wmake just uses the path as it is. TBH I think, if a change were to be made, it would be better to remove the `pwd -P` from the detection in bashrc#L46. This is how I build and I've added some commands to create a symlink to demonstrate the error: 8<--------------------------------------------------- BUILD_DIR=/scratch INSTALL_DIR=/apps # openfoam will get confused if the BUILD_DIR is a symlink cd $(readlink -f $BUILD_DIR) # # this is the part that adds a symlink to show the error # mkdir foo ln -s foo bar cd bar mkdir OpenFOAM cd OpenFOAM git clone git://github.com/OpenFOAM/OpenFOAM-6.git git clone git://github.com/OpenFOAM/ThirdParty-6.git export PATH=/usr/mpi/gcc/openmpi-4.0.2a1/bin:$PATH source OpenFOAM-6/etc/bashrc cd OpenFOAM-6 ./Allwmake -j 2>&1 | tee build.log --------------------------------------------------->8 This is the output: 8<--------------------------------------------------- ... wmakeLnInclude: linking include files to ./lnInclude Making dependency list for source file PstreamGlobals.C Making dependency list for source file UPstream.C Making dependency list for source file UIPread.C Making dependency list for source file UOPwrite.C g++ -std=c++11 -m64 -Dlinux64 -DWM_ARCH_OPTION=64 -DWM_DP -DWM_LABEL_SIZE=32 -Wall -Wextra -Wold-style-cast -Wnon-virtual-dtor -Wno-unused-parameter -Wno-invalid-offsetof -Wno-attributes -O3 -DNoRepository -ftemplate-depth-100 -DOMPI_SKIP_MPICXX -I/usr/mpi/gcc/openmpi-4.0.2a1/include/openmpi -I/usr/mpi/gcc/openmpi-4.0.2a1/include/openmpi/opal/mca/hwloc/hwloc201/hwloc/include -I/usr/mpi/gcc/openmpi-4.0.2a1/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/mpi/gcc/openmpi-4.0.2a1/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/mpi/gcc/openmpi-4.0.2a1/include -pthread -IlnInclude -I. -I/mnt/resource/scratch/foo/OpenFOAM/OpenFOAM-6/src/OpenFOAM/lnInclude -I/mnt/resource/scratch/foo/OpenFOAM/OpenFOAM-6/src/OSspecific/POSIX/lnInclude -fPIC -c UOPwrite.C -o Make/linux64GccDPInt32OptSYSTEMOPENMPI/UOPwrite.o g++ -std=c++11 -m64 -Dlinux64 -DWM_ARCH_OPTION=64 -DWM_DP -DWM_LABEL_SIZE=32 -Wall -Wextra -Wold-style-cast -Wnon-virtual-dtor -Wno-unused-parameter -Wno-invalid-offsetof -Wno-attributes -O3 -DNoRepository -ftemplate-depth-100 -DOMPI_SKIP_MPICXX -I/usr/mpi/gcc/openmpi-4.0.2a1/include/openmpi -I/usr/mpi/gcc/openmpi-4.0.2a1/include/openmpi/opal/mca/hwloc/hwloc201/hwloc/include -I/usr/mpi/gcc/openmpi-4.0.2a1/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/mpi/gcc/openmpi-4.0.2a1/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/mpi/gcc/openmpi-4.0.2a1/include -pthread -IlnInclude -I. -I/mnt/resource/scratch/foo/OpenFOAM/OpenFOAM-6/src/OpenFOAM/lnInclude -I/mnt/resource/scratch/foo/OpenFOAM/OpenFOAM-6/src/OSspecific/POSIX/lnInclude -fPIC -c UIPread.C -o Make/linux64GccDPInt32OptSYSTEMOPENMPI/UIPread.o g++ -std=c++11 -m64 -Dlinux64 -DWM_ARCH_OPTION=64 -DWM_DP -DWM_LABEL_SIZE=32 -Wall -Wextra -Wold-style-cast -Wnon-virtual-dtor -Wno-unused-parameter -Wno-invalid-offsetof -Wno-attributes -O3 -DNoRepository -ftemplate-depth-100 -DOMPI_SKIP_MPICXX -I/usr/mpi/gcc/openmpi-4.0.2a1/include/openmpi -I/usr/mpi/gcc/openmpi-4.0.2a1/include/openmpi/opal/mca/hwloc/hwloc201/hwloc/include -I/usr/mpi/gcc/openmpi-4.0.2a1/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/mpi/gcc/openmpi-4.0.2a1/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/mpi/gcc/openmpi-4.0.2a1/include -pthread -IlnInclude -I. -I/mnt/resource/scratch/foo/OpenFOAM/OpenFOAM-6/src/OpenFOAM/lnInclude -I/mnt/resource/scratch/foo/OpenFOAM/OpenFOAM-6/src/OSspecific/POSIX/lnInclude -fPIC -c UPstream.C -o Make/linux64GccDPInt32OptSYSTEMOPENMPI/UPstream.o g++ -std=c++11 -m64 -Dlinux64 -DWM_ARCH_OPTION=64 -DWM_DP -DWM_LABEL_SIZE=32 -Wall -Wextra -Wold-style-cast -Wnon-virtual-dtor -Wno-unused-parameter -Wno-invalid-offsetof -Wno-attributes -O3 -DNoRepository -ftemplate-depth-100 -DOMPI_SKIP_MPICXX -I/usr/mpi/gcc/openmpi-4.0.2a1/include/openmpi -I/usr/mpi/gcc/openmpi-4.0.2a1/include/openmpi/opal/mca/hwloc/hwloc201/hwloc/include -I/usr/mpi/gcc/openmpi-4.0.2a1/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/mpi/gcc/openmpi-4.0.2a1/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/mpi/gcc/openmpi-4.0.2a1/include -pthread -IlnInclude -I. -I/mnt/resource/scratch/foo/OpenFOAM/OpenFOAM-6/src/OpenFOAM/lnInclude -I/mnt/resource/scratch/foo/OpenFOAM/OpenFOAM-6/src/OSspecific/POSIX/lnInclude -fPIC -c PstreamGlobals.C -o Make/linux64GccDPInt32OptSYSTEMOPENMPI/PstreamGlobals.o g++ -std=c++11 -m64 -Dlinux64 -DWM_ARCH_OPTION=64 -DWM_DP -DWM_LABEL_SIZE=32 -Wall -Wextra -Wold-style-cast -Wnon-virtual-dtor -Wno-unused-parameter -Wno-invalid-offsetof -Wno-attributes -O3 -DNoRepository -ftemplate-depth-100 -DOMPI_SKIP_MPICXX -I/usr/mpi/gcc/openmpi-4.0.2a1/include/openmpi -I/usr/mpi/gcc/openmpi-4.0.2a1/include/openmpi/opal/mca/hwloc/hwloc201/hwloc/include -I/usr/mpi/gcc/openmpi-4.0.2a1/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/mpi/gcc/openmpi-4.0.2a1/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/mpi/gcc/openmpi-4.0.2a1/include -pthread -IlnInclude -I. -I/mnt/resource/scratch/foo/OpenFOAM/OpenFOAM-6/src/OpenFOAM/lnInclude -I/mnt/resource/scratch/foo/OpenFOAM/OpenFOAM-6/src/OSspecific/POSIX/lnInclude -fPIC -shared -Xlinker --add-needed -Xlinker --no-as-needed Make/linux64GccDPInt32OptSYSTEMOPENMPI/UOPwrite.o Make/linux64GccDPInt32OptSYSTEMOPENMPI/UIPread.o Make/linux64GccDPInt32OptSYSTEMOPENMPI/UPstream.o Make/linux64GccDPInt32OptSYSTEMOPENMPI/PstreamGlobals.o -L/mnt/resource/scratch/foo/OpenFOAM/OpenFOAM-6/platforms/linux64GccDPInt32OptSYSTEMOPENMPI/lib \ -pthread -Wl,-rpath -Wl,/usr/mpi/gcc/openmpi-4.0.2a1/lib64 -Wl,--enable-new-dtags -L/usr/mpi/gcc/openmpi-4.0.2a1/lib64 -lmpi -o /mnt/resource/scratch/foo/OpenFOAM/OpenFOAM-6/platforms/linux64GccDPInt32Opt/lib/openmpi-system/libPstream.so touch: cannot touch ‘/mnt/resource/scratch/foo/OpenFOAM/OpenFOAM-6/platforms/linux64GccDPInt32OptSYSTEMOPENMPI/src/Pstream/mpi/using:openmpi-system’: No such file or directory --------------------------------------------------->8 |
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> I think, if a change were to be made, it would be better to remove the `pwd -P` from the detection in bashrc#L46. This line has been changed over and over again and there is always some unusual installation configuration for which it causes problem. If we change it we would expect that many users installations would no longer compile and/or run. Does using expandPath "$PWD" if [ "$exPath" = "$WM_PROJECT_DIR" ] in wmake help? At least this change would be consistent with wclean. |
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This works for me: 8<---------------------------------------------------------- diff --git a/wmake/wmake b/wmake/wmake index 4836880..83abfab 100755 --- a/wmake/wmake +++ b/wmake/wmake @@ -395,10 +395,11 @@ fi #------------------------------------------------------------------------------ objectsDir=$MakeDir/$WM_OPTIONS -if [[ "$PWD" = *"$WM_PROJECT_DIR"* ]] +expandPath "$PWD" +if [[ "$exPath" = *"$WM_PROJECT_DIR"* ]] then platformPath=$WM_PROJECT_DIR/platforms/${WM_OPTIONS} - objectsDir=$platformPath${PWD//$WM_PROJECT_DIR/} + objectsDir=$platformPath${exPath//$WM_PROJECT_DIR/} fi ( ---------------------------------------------------------->8 |
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Resolved by commit 9980357df166e81b5d67fe6de33f9fff7869e373 |
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See https://bugs.openfoam.org/view.php?id=3303 |
| Date Modified | Username | Field | Change |
|---|---|---|---|
| 2019-07-02 08:29 | paulmedwards | New Issue | |
| 2019-07-02 08:58 | henry | Note Added: 0010538 | |
| 2019-07-02 09:02 | henry | Note Added: 0010539 | |
| 2019-07-02 09:44 | paulmedwards | Note Added: 0010541 | |
| 2019-07-02 09:52 | henry | Note Added: 0010543 | |
| 2019-07-02 10:29 | paulmedwards | Note Added: 0010545 | |
| 2019-07-02 11:59 | henry | Assigned To | => henry |
| 2019-07-02 11:59 | henry | Status | new => resolved |
| 2019-07-02 11:59 | henry | Resolution | open => fixed |
| 2019-07-02 11:59 | henry | Note Added: 0010547 | |
| 2019-07-16 10:05 | henry | Status | resolved => feedback |
| 2019-07-16 10:05 | henry | Resolution | fixed => reopened |
| 2019-07-16 10:05 | henry | Note Added: 0010572 | |
| 2019-07-16 10:05 | henry | Relationship added | related to 0003303 |
| 2020-01-07 11:28 | henry | Status | feedback => resolved |
