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January 25, 2013, 14:26 |
new user: compiling problems
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#1 |
Member
Tom Jentink
Join Date: Jan 2013
Posts: 61
Rep Power: 13 |
I just downloaded su2 and am trying to compile on a cluster here at NASA Langley that uses the module envrionment for desired packages.
When I enable mpi, tecplot, cgns, and metis, I am getting some c++ errors on int types. When I merely try the serial version (configure, make) with nothing special added, I get "omp.h" not found message. With the latter case, when all 4 packages are enabled, I have the intel_2011.9.293 module loaded, the tecplot module loaded, and the mpich2_intel module loaded. I am using mpicxx for the mpi compiler command. The config.log shows an error on conftest.cc: mpicxx -c -g -O2 conftest.cc >&5 error: identifier "exit" is undefined exit (42); When I run make, I get overloaded virtual function warnings: ------------------------------------------------------------------- then mv -f "../src/.deps/libSU2_a-geometry_structure.Tpo" "../src/.deps/libSU2_a-geometry_structure.Po"; else rm -f "../src/.deps/libSU2_a-geometry_structure.Tpo"; exit 1; fi ../src/../include/geometry_structure.hpp(580): warning #654: overloaded virtual function "CGeometry::SetVertex" is only partially overridden in class "CPhysicalGeometry" class CPhysicalGeometry : public CGeometry { ^ ---------------------------------------------------------------------------------------- and errors on type "int": -------------------------------------------------------------------------------------- ../src/geometry_structure.cpp(4298): error: argument of type "int *" is incompatible with parameter of type "idx_t={int64_t={long}} *" METIS_SetDefaultOptions(options); ^ |
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January 25, 2013, 14:27 |
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#2 |
Member
Tom Jentink
Join Date: Jan 2013
Posts: 61
Rep Power: 13 |
I forgot to add - my config line looks like this:
./configure CC="icpc -fargument-alias" --prefix=/u/tjentink/su2 --with-MPI=mpicxx --with-Tecio=/usr/local/pkgs-modules/tecplot360-2012R1_64_K2/lib --with-Metis-lib=/u/tjentink/su2/lib --with-Metis-include=/u/tjentink/su2/include --with-Metis-version=5 --with-CGNS-lib=/usr/local/pkgs-modules/cgnslib_3.1.3_64/lib --with-CGNS-include=/usr/local/pkgs-modules/cgnslib_3.1.3_64/include |
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January 28, 2013, 15:18 |
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#3 |
Super Moderator
Francisco Palacios
Join Date: Jan 2013
Location: Long Beach, CA
Posts: 404
Rep Power: 15 |
Thanks a lot for using our software.
We are aware of the warnings with the intel compilation (no warnings using gnu). But, it looks like a problem with the METIS version, which one are you using? Best, Francisco |
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January 28, 2013, 15:25 |
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#4 |
Member
Tom Jentink
Join Date: Jan 2013
Posts: 61
Rep Power: 13 |
Right now I am using version 5 of metis (see compile line above). The cluster I am using has a Metis module, but when I load it, I only get the library file - there is no include files. Should I download and use version 4?
Any idea why I can't compile in serial? When trying that, I get a message saying omp.h can't be found. |
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January 28, 2013, 15:28 |
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#5 | |
Super Moderator
Francisco Palacios
Join Date: Jan 2013
Location: Long Beach, CA
Posts: 404
Rep Power: 15 |
Quote:
Thanks! Francisco |
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January 28, 2013, 16:07 |
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#6 |
Member
Tom Jentink
Join Date: Jan 2013
Posts: 61
Rep Power: 13 |
I used Metis 4.0.3 and it all seemed to compile this time.
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January 28, 2013, 16:59 |
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#7 |
Member
Tom Jentink
Join Date: Jan 2013
Posts: 61
Rep Power: 13 |
When I try to run any of the pyton commands, I'm getting a syntax error when libSU2.py is imported.
File "/misc/home1/tjentink/su2/bin/libSU2.py", line 1289 except OSError as e: |
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January 29, 2013, 12:36 |
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#8 |
Member
Tom Jentink
Join Date: Jan 2013
Posts: 61
Rep Power: 13 |
python version issue. I switched to python 3.2 and this went away. However, the has_key attribute went away in version 3 of python. I had to replace all the d.has_key('a') instances in libSU2.py with 'a' in d.
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January 29, 2013, 13:43 |
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#9 |
Member
Tom Jentink
Join Date: Jan 2013
Posts: 61
Rep Power: 13 |
in mesh_adaptation.py, I had errors whenever the following occurs:
if save_all: print "Saving cycle" + ..... I had to put the line in parenthesis : if save_all: print ("Saving cycle" + .....) |
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January 29, 2013, 15:37 |
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#10 |
Super Moderator
Thomas D. Economon
Join Date: Jan 2013
Location: Stanford, CA
Posts: 271
Rep Power: 14 |
Just to follow up on some of these issues, since we're particularly interested in getting the code to compile on clusters...
Which version of Python was available on the cluster natively before switching to version 3.2? We have had success in the past with Python versions 2.6/2.7 and sometimes by installing a local copy of the free Enthought Python distribution (http://www.enthought.com/products/epd_free.php) that comes prepackaged with all of the modules that SU2 needs (NumPy, SciPy, etc.). |
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January 29, 2013, 15:44 |
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#11 | |
Member
Tom Jentink
Join Date: Jan 2013
Posts: 61
Rep Power: 13 |
Quote:
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