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OpenFOAM 2.2.2 on a cluster as a job FlexLexer error |
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November 28, 2013, 12:20 |
OpenFOAM 2.2.2 on a cluster as a job FlexLexer error
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#1 |
Senior Member
Artur
Join Date: May 2013
Location: Southampton, UK
Posts: 372
Rep Power: 19 |
Hi Foamers!
My university just started a new cluster so the first thing I tried was compiling the new OF there. From the log in node it works without any problems. However, I don't think running such big jobs is an elegant thing to do on a login node and so I used my script I had written for the previous cluster to compile OF as a sequential job. Here is the deal: running nodes don't have FlexLexer installed on them so to account for that I copy flex and flex++ into my own /bin directory and supply the header to OF via linking: ln -s /home/akl1g09/include/FlexLexer.h $FOAM_SRC/OpenFOAM/lnInclude/FlexLexer.h While it worked fine on the previous cluster on the new one I get the following error in the first lines of my log file: Code:
flex: error writing output file lex.yy.c Any advice will be appreciated A |
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November 29, 2013, 15:05 |
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#2 |
Retired Super Moderator
Bruno Santos
Join Date: Mar 2009
Location: Lisbon, Portugal
Posts: 10,974
Blog Entries: 45
Rep Power: 128 |
Greetings Artur,
OK, let's address this in parts:
Bruno
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December 2, 2013, 05:50 |
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#3 |
Senior Member
Artur
Join Date: May 2013
Location: Southampton, UK
Posts: 372
Rep Power: 19 |
Hi Bruno,
Thanks for your reply. I set my script up so that it does the compilation in my home directory so that then I can just source the foam dot file from my .bash_profile when I log in (just as you say, it is enough to have the compiled source on my log in node). When I ran it on the previous cluster just by running ./Allwmake from terminal upon ssh'ing to the server it was running painfully slowly so I wrote a script which submits the whole process as a job (not to overload the log in nodes and to be able to work while it's running). In order to do that I had to do the flexlexer trick with copying it to my home/bin and linking the header for OF to see it. On the new cluster I did the same and I get the error listed previously, here's the surrounding bit of the log (literally very beginning): Code:
gcc -m64 -Wall -O3 -fPIC dirToString.c -o /home/akl1g09/OpenFOAM/OpenFOAM-2.2.2/wmake/platforms/linux64Gcc/dirToString flex wmkdep.l flex: fatal internal error, exec failed flex: error writing output file lex.yy.c make: *** [/home/akl1g09/OpenFOAM/OpenFOAM-2.2.2/wmake/platforms/linux64Gcc/wmkdep] Error 1 All the best, Artur |
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December 8, 2013, 14:13 |
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#4 | |
Retired Super Moderator
Bruno Santos
Join Date: Mar 2009
Location: Lisbon, Portugal
Posts: 10,974
Blog Entries: 45
Rep Power: 128 |
Hi Artur,
Well, it looks like the job is not able to access the path with write capabilities, as this implies: Quote:
Best regards, Bruno
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December 8, 2013, 15:28 |
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#5 |
Senior Member
Artur
Join Date: May 2013
Location: Southampton, UK
Posts: 372
Rep Power: 19 |
Hi Bruno,
Thanks for clearing this up for me. I'll just stick to compiling it from the log-in node then. Have a nice day, A |
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