0000961: transformPoints does not accept options when run with foamjob

ID	Project	Category	View Status	Date Submitted	Last Update

0000961	OpenFOAM	Bug	public	2013-08-14 12:25	2013-11-27 14:24

Reporter	rperry	Assigned To	~~user4~~
Priority	high	Severity	minor	Reproducibility	always
Status	resolved	Resolution	fixed
Platform	Suse 10

Summary	0000961: transformPoints does not accept options when run with foamjob
Description	Take any decomposed mesh from snappy, and runing transform points using mpirun will transform them acceptably, and it will accept transformPoints options like -scale '(0.001 0.001 0.001)' However, using foamjob to execute the same option will raise the error "invalid number of inputs, expected 0 received 2" It appears that with foamJob, no inputs are accepted, even though transformPoints requires at minimum one input in order to do anything. At first I thought it was just having issues accepting the vector input shown above, but indeed it does not accept any inputs.
Tags	No tags attached.

wyldckat 2013-08-14 21:21 updater ~0002413 Last edited: 2013-08-14 21:22	This is related to the bug report #668: http://www.openfoam.org/mantisbt/view.php?id=668 Attached is a patch that fixes this. In essence, it's a matter of wrapping $@ in quotes, namely: "$@" The only problem is that I could not find a way to echo properly the command that should be used, so it will appear to still be broken, but it will work as intended. Example: $ foamJob transformPoints -translate '(1 0 0)' Application : transformPoints Executing: /home/user/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/bin/transformPoints -translate (1 0 0) > log 2>&1 &

wyldckat 2013-08-14 21:21 updater	foamJob.patch (994 bytes) diff --git a/bin/foamJob b/bin/foamJob index 4eda404..87c4392 100755 --- a/bin/foamJob +++ b/bin/foamJob @@ -218,10 +218,10 @@ then if [ "$screenOpt" = true ] then echo "Executing: $mpirun $mpiopts $APPLICATION $@ -parallel \| tee log" - $mpirun $mpiopts $APPLICATION $@ -parallel \| tee log + $mpirun $mpiopts $APPLICATION "$@" -parallel \| tee log else echo "Executing: $mpirun $mpiopts $APPLICATION $@ -parallel > log 2>&1" - $mpirun $mpiopts $APPLICATION $@ -parallel > log 2>&1 & + $mpirun $mpiopts $APPLICATION "$@" -parallel > log 2>&1 & fi else @@ -231,11 +231,11 @@ else if [ "$screenOpt" = true ] then echo "Executing: $APPLICATION $@ \| tee log &" - $APPLICATION $@ \| tee log & + $APPLICATION "$@" \| tee log & wait $! else echo "Executing: $APPLICATION $@ > log 2>&1 &" - $APPLICATION $@ > log 2>&1 & + $APPLICATION "$@" > log 2>&1 & fi fi foamJob.patch (994 bytes)

~~user258~~ 2013-08-21 11:50 ~0002433	What do you mean by "The only problem is that I could not find a way to echo properly the command that should be used". It is printing the application only, which the intended output. In other words, what is wrong with your example?

wyldckat 2013-08-21 14:05 updater ~0002434	Ah, I see that your eyes are not yet fully trained in the ways of the shell ;) If you try to run the command that foamJob tells us it's using, namely this: transformPoints -translate (1 0 0) > log 2>&1 & the shell (sh or bash) will complain about the sub-shell that is started with the parenthesis, namely: (1 0 0) where the complain is likely be because "1" is not a valid command. Which is why we have to use the single quotes: transformPoints -translate '(1 0 0)' > log 2>&1 & But since foamJob is using the "echo" command to show us what it's going to run, the single quotes are "taken out of the picture".

~~user258~~ 2013-08-21 15:25 ~0002435	Ha, if you make that mistake often you might spot it more easily indeed. Anyhow, challenge accepted, and this ugly code snippet might work :): echo -n "Executing: $APPLICATION" for v in "$@"; do if [[ "${v##* }" == "$v" ]]; then echo -n " $v" else echo -n " '$v'" fi done; echo " > log 2>&1 &"

wyldckat 2013-08-25 18:40 updater	foamJob.v2.patch (1,860 bytes) diff --git a/bin/foamJob b/bin/foamJob index 4eda404..24f7d48 100755 --- a/bin/foamJob +++ b/bin/foamJob @@ -50,6 +50,28 @@ USAGE exit 1 } +#for being able to echo strings that have single quotes +echoArgs() { + addSpace="" + + for stringItem in "$@"; do + + echo -n "${addSpace}" + + if [ "${stringItem##* }" = "$stringItem" ] + then + echo -n "$stringItem" + addSpace=" " + else + echo -n "'$stringItem'" + addSpace=" " + fi + + done + + unset stringItem addSpace +} + unset version # replacement for possibly buggy 'which' @@ -217,11 +239,11 @@ then # if [ "$screenOpt" = true ] then - echo "Executing: $mpirun $mpiopts $APPLICATION $@ -parallel \| tee log" - $mpirun $mpiopts $APPLICATION $@ -parallel \| tee log + echo "Executing: $mpirun $mpiopts $APPLICATION $(echoArgs "$@") -parallel \| tee log" + $mpirun $mpiopts $APPLICATION "$@" -parallel \| tee log else - echo "Executing: $mpirun $mpiopts $APPLICATION $@ -parallel > log 2>&1" - $mpirun $mpiopts $APPLICATION $@ -parallel > log 2>&1 & + echo "Executing: $mpirun $mpiopts $APPLICATION $(echoArgs "$@") -parallel > log 2>&1" + $mpirun $mpiopts $APPLICATION "$@" -parallel > log 2>&1 & fi else @@ -230,12 +252,12 @@ else # if [ "$screenOpt" = true ] then - echo "Executing: $APPLICATION $@ \| tee log &" - $APPLICATION $@ \| tee log & + echo "Executing: $APPLICATION $(echoArgs "$@") \| tee log &" + $APPLICATION "$@" \| tee log & wait $! else - echo "Executing: $APPLICATION $@ > log 2>&1 &" - $APPLICATION $@ > log 2>&1 & + echo "Executing: $APPLICATION $(echoArgs "$@") > log 2>&1 &" + $APPLICATION "$@" > log 2>&1 & fi fi foamJob.v2.patch (1,860 bytes)

wyldckat 2013-08-25 18:44 updater ~0002438	@bernhardr: Nice hack! The attached patch file "foamJob.v2.patch" includes bernhardr's adapted code snippet. The adaptation uses "sh" if-statements instead of "bash" if-statements and uses a function named "echoArgs" for using echo in a dedicated manner for the "$@". The modified code was tested on Ubuntu 12.04, using for "sh" the "dash" shell.

rperry 2013-11-27 10:04 reporter ~0002661	I have found the same issue exists with the orientFaceZone utility - you cannot give orientFaceZone the coordinate point input it requires using foamJob. Is there any way both of these issues can be resolved in the core openFOAM repository?

wyldckat 2013-11-27 10:20 updater ~0002662	@rperry: Have you tested whether any of the provided patches in attachment work for you?

rperry 2013-11-27 10:48 reporter ~0002663	Hi wyldckat, your first patch worked for all the utilities I was having problems with. I just realized the reason I had this problem again today was that I was on a system that had recently had OpenFOAM installed, and thus didn't have the patch applied :-P Will this fix be included at some point in the standard release of OpenFOAM?

~~user4~~ 2013-11-27 14:24 ~0002664	c7b2d61927b00fc26a6e0f53e41b7ea48a184c04 Thanks for fix.

Date Modified	Username	Field	Change
2013-08-14 12:25	rperry	New Issue
2013-08-14 21:21	wyldckat	Note Added: 0002413
2013-08-14 21:21	wyldckat	File Added: foamJob.patch
2013-08-14 21:22	wyldckat	Note Edited: 0002413
2013-08-21 11:50	~~user258~~	Note Added: 0002433
2013-08-21 14:05	wyldckat	Note Added: 0002434
2013-08-21 15:25	~~user258~~	Note Added: 0002435
2013-08-25 18:40	wyldckat	File Added: foamJob.v2.patch
2013-08-25 18:44	wyldckat	Note Added: 0002438
2013-11-27 10:04	rperry	Note Added: 0002661
2013-11-27 10:20	wyldckat	Note Added: 0002662
2013-11-27 10:48	rperry	Note Added: 0002663
2013-11-27 14:24	~~user4~~	Note Added: 0002664
2013-11-27 14:24	~~user4~~	Status	new => resolved
2013-11-27 14:24	~~user4~~	Fixed in Version	=> 2.2.x
2013-11-27 14:24	~~user4~~	Resolution	open => fixed
2013-11-27 14:24	~~user4~~	Assigned To	=> user4

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