CFD Online Logo CFD Online URL
www.cfd-online.com
[Sponsors]
Home > Forums > Software User Forums > SU2 > SU2 Installation

new user: compiling problems

Register Blogs Members List Search Today's Posts Mark Forums Read

Reply
 
LinkBack Thread Tools Search this Thread Display Modes
Old   January 25, 2013, 14:26
Default new user: compiling problems
  #1
Member
 
Tom Jentink
Join Date: Jan 2013
Posts: 61
Rep Power: 13
jentink is on a distinguished road
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);
^
jentink is offline   Reply With Quote

Old   January 25, 2013, 14:27
Default
  #2
Member
 
Tom Jentink
Join Date: Jan 2013
Posts: 61
Rep Power: 13
jentink is on a distinguished road
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
jentink is offline   Reply With Quote

Old   January 28, 2013, 15:18
Default
  #3
Super Moderator
 
Francisco Palacios
Join Date: Jan 2013
Location: Long Beach, CA
Posts: 404
Rep Power: 15
fpalacios is on a distinguished road
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
fpalacios is offline   Reply With Quote

Old   January 28, 2013, 15:25
Default
  #4
Member
 
Tom Jentink
Join Date: Jan 2013
Posts: 61
Rep Power: 13
jentink is on a distinguished road
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.
jentink is offline   Reply With Quote

Old   January 28, 2013, 15:28
Default
  #5
Super Moderator
 
Francisco Palacios
Join Date: Jan 2013
Location: Long Beach, CA
Posts: 404
Rep Power: 15
fpalacios is on a distinguished road
Quote:
Originally Posted by jentink View Post
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.
I'm gonna try with metis 5.0 but, for the time being, could you please try with metis-4.0.3?

Thanks!
Francisco
fpalacios is offline   Reply With Quote

Old   January 28, 2013, 16:07
Default
  #6
Member
 
Tom Jentink
Join Date: Jan 2013
Posts: 61
Rep Power: 13
jentink is on a distinguished road
I used Metis 4.0.3 and it all seemed to compile this time.
jentink is offline   Reply With Quote

Old   January 28, 2013, 16:59
Default
  #7
Member
 
Tom Jentink
Join Date: Jan 2013
Posts: 61
Rep Power: 13
jentink is on a distinguished road
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:
jentink is offline   Reply With Quote

Old   January 29, 2013, 12:36
Default
  #8
Member
 
Tom Jentink
Join Date: Jan 2013
Posts: 61
Rep Power: 13
jentink is on a distinguished road
Quote:
Originally Posted by jentink View Post
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:
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.
jentink is offline   Reply With Quote

Old   January 29, 2013, 13:43
Default
  #9
Member
 
Tom Jentink
Join Date: Jan 2013
Posts: 61
Rep Power: 13
jentink is on a distinguished road
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" + .....)
jentink is offline   Reply With Quote

Old   January 29, 2013, 15:37
Default
  #10
Super Moderator
 
Thomas D. Economon
Join Date: Jan 2013
Location: Stanford, CA
Posts: 271
Rep Power: 14
economon is on a distinguished road
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.).
economon is offline   Reply With Quote

Old   January 29, 2013, 15:44
Default
  #11
Member
 
Tom Jentink
Join Date: Jan 2013
Posts: 61
Rep Power: 13
jentink is on a distinguished road
Quote:
Originally Posted by economon View Post
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.).
default version on the cluster I'm using is 2.4.2. they had a 3.2.2 module available to load. that's the one I'm currently using.
jentink is offline   Reply With Quote

Reply

Thread Tools Search this Thread
Search this Thread:

Advanced Search
Display Modes

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off
Trackbacks are Off
Pingbacks are On
Refbacks are On


Similar Threads
Thread Thread Starter Forum Replies Last Post
problems on multi-file udf compiling phoenixchen903 FLUENT 1 August 30, 2009 03:35
Problems with User Defined Scalar Alberto Cuoci FLUENT 0 June 26, 2007 15:55
Problems compiling UDFs under SuSE 10.2 George FLUENT 1 February 21, 2007 09:36
Problems with compiling CFD code! ravi Main CFD Forum 1 July 12, 2004 12:28
CFX 5.5 Roued CFX 1 October 2, 2001 17:49


All times are GMT -4. The time now is 16:02.