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Kubuntu uses dash breaks All scripts in tutorials |
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March 30, 2008, 11:30 |
(K)ubuntu versions since Edgy,
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#1 |
Member
Graeme Cottrell
Join Date: Mar 2009
Posts: 30
Rep Power: 17 |
(K)ubuntu versions since Edgy, including Gutsy, which I am using, use dash as the default shell:
graeme@graeme-vaio:/bin$ ls -l /bin/sh* lrwxrwxrwx 1 root root 4 2007-10-31 05:02 /bin/sh -> dash lrwxrwxrwx 1 root root 4 2007-10-31 05:02 /bin/sh.distrib -> bash graeme@graeme-vaio:/bin$ I'm not sure what the symlink /bin/sh.distrib is used for. This use of dash causes problems with Allrun, Allclean and other scripts in the tutorials directory tree. Replacing the shebangs in the scripts with #!/bin/bash makes the problems seem to go away. I don't know exactly where they trip up, but here's an example of running Allrun in the icoFoam directory after a fresh install of the tutorials: graeme@graeme-vaio:~/OpenFOAM/graeme-1.4.1/run/tutorials/icoFoam$ ./Allrun Running blockMesh on cavity Running icoFoam on cavity Cloning cavityFine case from cavity cp: cannot stat `cavity/{0,system,constant}': No such file or directory sed: can't read cavityFine/constant/polyMesh/blockMeshDict: No such file or directory mv: cannot move `temp.24790' to `cavityFine/constant/polyMesh/blockMeshDict': No such file or directory sed: can't read cavityFine/system/controlDict: No such file or directory mv: cannot move `temp.24790' to `cavityFine/system/controlDict': No such file or directory Running blockMesh on cavityFine Running mapFields from cavity to cavityFine Running icoFoam on cavityFine Running blockMesh on cavityGrade Running mapFields from cavityFine to cavityGrade Running icoFoam on cavityGrade Cloning cavityHighRe case from cavity cp: cannot stat `cavity/{0,system,constant}': No such file or directory Setting cavityHighRe to generate a secondary vortex sed: can't read cavityHighRe/system/controlDict: No such file or directory mv: cannot move `temp.24790' to `cavityHighRe/system/controlDict': No such file or directory sed: can't read cavityHighRe/constant/transportProperties: No such file or directory mv: cannot move `temp.24790' to `cavityHighRe/constant/transportProperties': No such file or directory Copying cavity/0* directory to cavityHighRe Running blockMesh on cavityHighRe Running icoFoam on cavityHighRe Running blockMesh on cavityClipped Running mapFields from cavity to cavityClipped Running icoFoam on cavityClipped fluentMeshToFoam: converting mesh elbow/elbow.msh Running icoFoam on elbow Running foamMeshToFluent on elbow Running foamDataToFluent on elbow graeme@graeme-vaio:~/OpenFOAM/graeme-1.4.1/run/tutorials/icoFoam$ then running Allclean: graeme@graeme-vaio:~/OpenFOAM/graeme-1.4.1/run/tutorials/icoFoam$ ./Allclean Cleaning cavity case of icoFoam application ./Allclean: 18: let: not found ./Allclean: 18: let: not found ./Allclean: 18: let: not found ./Allclean: 18: let: not found ./Allclean: 18: let: not found ... ad infinitum Replacing the symlink at /bin/sh to point to bash seems to be an option, but I am reluctant to make such a system-wide change for the sake of OpenFOAM - I don't know what else might break. Replacing the shebangs in the scripts to use bash gives: graeme@graeme-vaio:~/OpenFOAM/graeme-1.4.1/run/tutorials/icoFoam$ ./Allrun Running blockMesh on cavity Running icoFoam on cavity Cloning cavityFine case from cavity Running blockMesh on cavityFine Running mapFields from cavity to cavityFine Running icoFoam on cavityFine Running blockMesh on cavityGrade Running mapFields from cavityFine to cavityGrade Running icoFoam on cavityGrade Cloning cavityHighRe case from cavity Setting cavityHighRe to generate a secondary vortex Copying cavity/0* directory to cavityHighRe Running blockMesh on cavityHighRe Running icoFoam on cavityHighRe Running blockMesh on cavityClipped Running mapFields from cavity to cavityClipped Running icoFoam on cavityClipped fluentMeshToFoam: converting mesh elbow/elbow.msh Running icoFoam on elbow Running foamMeshToFluent on elbow Running foamDataToFluent on elbow graeme@graeme-vaio:~/OpenFOAM/graeme-1.4.1/run/tutorials/icoFoam$ and for Allclean: graeme@graeme-vaio:~/OpenFOAM/graeme-1.4.1/run/tutorials/icoFoam$ ./Allclean Cleaning cavity case of icoFoam application Cleaning cavityGrade case of icoFoam application Cleaning cavityClipped case of icoFoam application Cleaning elbow case of icoFoam application Removing cavityFine case of icoFoam application Removing cavityHighRe case of icoFoam application graeme@graeme-vaio:~/OpenFOAM/graeme-1.4.1/run/tutorials/icoFoam$ I assume these are the correct outputs for these cases. Perhaps the scripts aren't quite POSIX conformant, or perhaps dash has bugs - I don't know. I do know that the Ubuntu variants have a huge user base and some of those users are going to want to run OpenFOAM. Other novices are going to trip over this problem and not know what to do. I see no previous reference to this in the forums here. Anyone got any comments or suggestions? Someone like to whip up a quick script that will automate the changing of the shebangs? |
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March 30, 2008, 12:09 |
A follow-up. I just found the
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#2 |
Member
Graeme Cottrell
Join Date: Mar 2009
Posts: 30
Rep Power: 17 |
A follow-up. I just found the tool checkbashisms (in the devscripts package) which reports on CleanFunctions thus:
graeme@graeme-vaio:~/OpenFOAM/graeme-1.4.1/run/tutorials$ checkbashisms CleanFunctions possible bashism in CleanFunctions line 57 (let ...): let nZeros=nZeros+1 possible bashism in CleanFunctions line 59 (brace expansion): rm -rf $1/{[1-9]*,-[1-9]*,log,log.*,log-*,logSummary.*,.fxLock,*.xml,ParaView*,paraFoam *,*.foam} > /dev/null 2>&1 possible bashism in CleanFunctions line 66 (brace expansion): rm -rf $1/constant/polyMesh/{allOwner*,cell*,face*,meshModifiers*} \ possible bashism in CleanFunctions line 67 (brace expansion): $1/constant/polyMesh/{owner*,neighbour*,point*,edge*} \ possible bashism in CleanFunctions line 92 (brace expansion): rm -rf $1/{samples,sampleSurfaces} > /dev/null 2>&1 possible bashism in CleanFunctions line 97 (brace expansion): rm -rf $1/0/{Ux,Uy,Uz} > /dev/null 2>&1 graeme@graeme-vaio:~/OpenFOAM/graeme-1.4.1/run/tutorials$ and on RunFunctions like this: graeme@graeme-vaio:~/OpenFOAM/graeme-1.4.1/run/tutorials$ checkbashisms RunFunctions possible bashism in RunFunctions line 77 (brace expansion): cp -r $1/{0,system,constant} $2 graeme@graeme-vaio:~/OpenFOAM/graeme-1.4.1/run/tutorials$ The brace expansions may be easy enough to remove, but what about the let statement? Is there a POSIX compliant way to do that sort of arithmetic? |
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March 30, 2008, 16:06 |
More progress.
I have a bas
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#3 |
Member
Graeme Cottrell
Join Date: Mar 2009
Posts: 30
Rep Power: 17 |
More progress.
I have a bash script, using find and sed, that replaces the shebangs with #!/bin/bash. I'm calling it InitTuts, and the current version destroys any existing tutorial data that you've been working on, makes a new copy of the tutorials in the correct place, then systematically modifies the scripts. Create InitTuts in $HOME/OpenFOAM/${LOGNAME}-1.4.1/run, make it executable and then make sure you're not using the tutorial directories in any way, then just run it. YMMV. #!/bin/bash cd $HOME/OpenFOAM/${LOGNAME}-1.4.1/run echo Removing existing tutorial data rm -rf $HOME/OpenFOAM/${LOGNAME}-1.4.1/run/tutorials echo Making a fresh copy of the tutorials from $WM_PROJECT_DIR/tutorials cp -r $WM_PROJECT_DIR/tutorials $HOME/OpenFOAM/${LOGNAME}-1.4.1/run scripts="Allclean Allrun Alltest CleanFunctions RunFunctions" echo Processing shebangs in scripts to explicitly reference /bin/bash for script in $scripts do echo processing for $script scripts find $HOME/OpenFOAM/${LOGNAME}-1.4.1/run/tutorials \ -name $script -execdir sed -i s/"#!\/bin\/sh"/"#!\/bin\/bash"/ $script \; done echo done. |
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March 30, 2008, 16:41 |
Added a brief reference to thi
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#4 |
Member
Graeme Cottrell
Join Date: Mar 2009
Posts: 30
Rep Power: 17 |
Added a brief reference to this in the wiki.
If anyone comes up with a better solution, please make youself heard. |
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March 31, 2008, 17:34 |
Strange, I built stock OF 1.4.
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#5 |
Senior Member
Srinath Madhavan (a.k.a pUl|)
Join Date: Mar 2009
Location: Edmonton, AB, Canada
Posts: 703
Rep Power: 21 |
Strange, I built stock OF 1.4.1 on Gutsy and never faced any problems.
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March 31, 2008, 17:35 |
Oh, just noticed. You meant tu
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#6 |
Senior Member
Srinath Madhavan (a.k.a pUl|)
Join Date: Mar 2009
Location: Edmonton, AB, Canada
Posts: 703
Rep Power: 21 |
Oh, just noticed. You meant tutorials. OK. That could be possible. I only run my own cases these days.
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April 1, 2008, 15:44 |
Hi Graeme,
looks like you a
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#7 |
Senior Member
Mattijs Janssens
Join Date: Mar 2009
Posts: 1,419
Rep Power: 26 |
Hi Graeme,
looks like you are right - we seem to be using bash extensions instead of pure Posix. I'll have a look. |
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April 15, 2008, 08:42 |
Hi, "similar" shell-thing in m
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#8 |
Member
Niklas Wikstrom
Join Date: Mar 2009
Posts: 86
Rep Power: 17 |
Hi, "similar" shell-thing in most csh scripts on Ubuntu:
Description: Running a csh script including e.g. a 'number of args'-test like in foamNew: if ( $# != 2 ) then result in Illegal variable name Solver/Application: csh-scripts in $WM_PROJECT_DIR/bin/ Source file: E.G. $WM_PROJECT_DIR/bin/foamNew Testcase: any Platform: Ubuntu Linux 8.* Version: 1.4.1 Notes: Easily corrected by changing $# to $* or $argv[*] cd $WM_PROJECT_DIR/bin for file in $(egrep -l "^#\!.*csh"; do echo $file sed -i_bak -e 's/$#/$argv[\*]/g' $file done |
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April 15, 2008, 08:52 |
Oh, seems only to be foamNew t
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#9 |
Member
Niklas Wikstrom
Join Date: Mar 2009
Posts: 86
Rep Power: 17 |
Oh, seems only to be foamNew that is affected by this, since most other scripts ar sh and not csh.
and in the "fix" above a parenthesis is missing. Use only: sed -i_bak -e 's/$#/$argv[\*]/g' foamNew |
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