Hello,
I have been looking through past discussions, but am still unable to get CS and Syrthes working together. Perhaps my linux skills are not solid enough to follow, given the level of detail in postings.
I've tried:
1. fresh installation in Ubuntu 10.04
2. using CAElinux 2010
I'm certainly open to using a different linux distribution, if there is one that is easier to get working.
I began by going a tutorial posted here on CS and Syrthes, using an installation of CAElinux 2010. CS stalled with no CPU activity after a syrthes compilation error. Based on the output of 'code_saturne config', CS was not installed correctly to recognize Syrthes(?).
If anyone has experience getting this working in CAElinux 2010, or any easier way to get a working installation, please advise.
Thanks
Andy
CS and Syrthes, fresh installation or CAElinux 2010?
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-
Yvan Fournier
Re: CS and Syrthes, fresh installation or CAElinux 2010?
Hello,
Both should work, though we have not tested the latest CAElinux.
Did you use the compilation script, or did you install components manually ? Which versions are you using ?
Could you post your install and error logs ?
Best regards,
Yvan
Both should work, though we have not tested the latest CAElinux.
Did you use the compilation script, or did you install components manually ? Which versions are you using ?
Could you post your install and error logs ?
Best regards,
Yvan
-
Andrew Miner
Re: CS and Syrthes, fresh installation or CAElinux 2010?
Hello,
I have been pursuing a third option that was recommended at code-saturne.blogspot.com by an anonymous poster. Using Ubuntu 10.10, and installing CS by apt. CS installs with Syrthes. The version is rc1. The output from code_saturn config is:
Directories:
dirs.prefix = /usr
dirs.exec_prefix = /usr
dirs.bindir = /usr/bin
dirs.includedir = /usr/include
dirs.libdir = /usr/lib
dirs.datarootdir = /usr/share
dirs.datadir = /usr/share
dirs.pkgdatadir = /usr/share/ncs
dirs.docdir = /usr/share/doc/ncs
dirs.pdfdir = /usr/share/doc/ncs
Auxiliary information:
dirs.ecs_bindir = /usr/bin
dirs.syrthes_prefix = /usr/lib/syrthes/3.4.2
MPI library information:
mpi_lib.type =
mpi_lib.bindir =
mpi_lib.libdir =
Compilers and associated options:
cc = gcc
fc = gfortran
cppflags = -D_POSIX_SOURCE -DNDEBUG -I/usr/include/libxml2
cflags = -std=c99 -funsigned-char -pedantic -W -Wall -Wshadow -Wpointer-arith -Wcast-qual -Wcast-align -Wwrite-strings -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wnested-externs -Wunused -Wfloat-equal -g -O2 -g -Wall -O2 -funroll-loops -O2 -Wuninitialized -march=i686
fcflags = -x f95-cpp-input -Wall -Wno-unused -D_CS_FC_HAVE_FLUSH -O
ldflags = -Wl,-export-dynamic -Wl,-Bsymbolic-functions -O
libs = -lfvm -lm -lcgns -lhdf5 -lmei -lbft -lz -lxml2 -lblas -L/usr/lib/gcc/i686-linux-gnu/4.4.5 -L/usr/lib/gcc/i686-linux-gnu/4.4.5/../../../../lib -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/i686-linux-gnu/4.4.5/../../.. -lgfortranbegin -lgfortran -lm -ldl
rpath = -Wl,-rpath -Wl,
Compilers and associated options for SYRTHES build:
cc = /usr/bin/gcc
fc = /usr/bin/gfortran
cppflags = -I/usr/lib/syrthes/3.4.2/include
cflags = -O2 -D_FILE_OFFSET_BITS=64 -DHAVE_C_IO
fcflags = -O2 -DHAVE_C_IO -D_FILE_OFFSET_BITS=64
ldflags = -L/usr/lib/syrthes/3.4.2/lib/Linux
libs = -lbft -lz -lsatsyrthes3.4.2_Linux -lsyrthes3.4.2_Linux -L/usr/lib/gcc/i686-linux-gnu/4.4.5 -L/usr/lib/gcc/i686-linux-gnu/4.4.5/../../../../lib -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/i686-linux-gnu/4.4.5/../../.. -lgfortranbegin -lgfortran -l
With this installed, I again tried to walk through Brennan's tutorials at:
http://code-saturne.org/forum/viewtopic.php?f=10&t=944
There is an error right away. It looks like this installation via apt may not have the MED option. Here is the output when I run Brennan's first example, case1:
Single processor Code_Saturne simulation
Code_Saturne is running
***********************
Working directory (to be periodically cleaned) :
/home/miner/tmp_Saturne/miner.CASE1.01170838
Kernel version: /usr
Preprocessor: /usr/bin
********************************************
Preparing calculation
********************************************
********************************************
Starting calculation
********************************************
Error running the preprocessor.
Check preprocessor log (listpre) for details.
********************************************
Error in preprocessing stage.
********************************************
The output of listpre indicates the problem with the MED installation:
Error in ECS execution
======================
ecs_pre.c:385: Fatal error.
File format "MED" support not available in this
installation (file "Mesh_fluid.med").
Call stack
1: 0x7f03f00d2340 <bft_error+0x80> (libbft.so.1)
2: 0x40b7fb <> (cs_preprocess)
3: 0x407435 <> (cs_preprocess)
4: 0x407f36 <> (cs_preprocess)
5: 0x7f03eee7bd8e <__libc_start_main+0xfe> (libc.so.6)
6: 0x4032c9 <> (cs_preprocess)
End of stack
How can I find out if the MED option was set upon CS installation? May not have been.
I have been pursuing a third option that was recommended at code-saturne.blogspot.com by an anonymous poster. Using Ubuntu 10.10, and installing CS by apt. CS installs with Syrthes. The version is rc1. The output from code_saturn config is:
Directories:
dirs.prefix = /usr
dirs.exec_prefix = /usr
dirs.bindir = /usr/bin
dirs.includedir = /usr/include
dirs.libdir = /usr/lib
dirs.datarootdir = /usr/share
dirs.datadir = /usr/share
dirs.pkgdatadir = /usr/share/ncs
dirs.docdir = /usr/share/doc/ncs
dirs.pdfdir = /usr/share/doc/ncs
Auxiliary information:
dirs.ecs_bindir = /usr/bin
dirs.syrthes_prefix = /usr/lib/syrthes/3.4.2
MPI library information:
mpi_lib.type =
mpi_lib.bindir =
mpi_lib.libdir =
Compilers and associated options:
cc = gcc
fc = gfortran
cppflags = -D_POSIX_SOURCE -DNDEBUG -I/usr/include/libxml2
cflags = -std=c99 -funsigned-char -pedantic -W -Wall -Wshadow -Wpointer-arith -Wcast-qual -Wcast-align -Wwrite-strings -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wnested-externs -Wunused -Wfloat-equal -g -O2 -g -Wall -O2 -funroll-loops -O2 -Wuninitialized -march=i686
fcflags = -x f95-cpp-input -Wall -Wno-unused -D_CS_FC_HAVE_FLUSH -O
ldflags = -Wl,-export-dynamic -Wl,-Bsymbolic-functions -O
libs = -lfvm -lm -lcgns -lhdf5 -lmei -lbft -lz -lxml2 -lblas -L/usr/lib/gcc/i686-linux-gnu/4.4.5 -L/usr/lib/gcc/i686-linux-gnu/4.4.5/../../../../lib -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/i686-linux-gnu/4.4.5/../../.. -lgfortranbegin -lgfortran -lm -ldl
rpath = -Wl,-rpath -Wl,
Compilers and associated options for SYRTHES build:
cc = /usr/bin/gcc
fc = /usr/bin/gfortran
cppflags = -I/usr/lib/syrthes/3.4.2/include
cflags = -O2 -D_FILE_OFFSET_BITS=64 -DHAVE_C_IO
fcflags = -O2 -DHAVE_C_IO -D_FILE_OFFSET_BITS=64
ldflags = -L/usr/lib/syrthes/3.4.2/lib/Linux
libs = -lbft -lz -lsatsyrthes3.4.2_Linux -lsyrthes3.4.2_Linux -L/usr/lib/gcc/i686-linux-gnu/4.4.5 -L/usr/lib/gcc/i686-linux-gnu/4.4.5/../../../../lib -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/i686-linux-gnu/4.4.5/../../.. -lgfortranbegin -lgfortran -l
With this installed, I again tried to walk through Brennan's tutorials at:
http://code-saturne.org/forum/viewtopic.php?f=10&t=944
There is an error right away. It looks like this installation via apt may not have the MED option. Here is the output when I run Brennan's first example, case1:
Single processor Code_Saturne simulation
Code_Saturne is running
***********************
Working directory (to be periodically cleaned) :
/home/miner/tmp_Saturne/miner.CASE1.01170838
Kernel version: /usr
Preprocessor: /usr/bin
********************************************
Preparing calculation
********************************************
********************************************
Starting calculation
********************************************
Error running the preprocessor.
Check preprocessor log (listpre) for details.
********************************************
Error in preprocessing stage.
********************************************
The output of listpre indicates the problem with the MED installation:
Error in ECS execution
======================
ecs_pre.c:385: Fatal error.
File format "MED" support not available in this
installation (file "Mesh_fluid.med").
Call stack
1: 0x7f03f00d2340 <bft_error+0x80> (libbft.so.1)
2: 0x40b7fb <> (cs_preprocess)
3: 0x407435 <> (cs_preprocess)
4: 0x407f36 <> (cs_preprocess)
5: 0x7f03eee7bd8e <__libc_start_main+0xfe> (libc.so.6)
6: 0x4032c9 <> (cs_preprocess)
End of stack
How can I find out if the MED option was set upon CS installation? May not have been.
-
Brennan Sharp
Re: CS and Syrthes, fresh installation or CAElinux 2010?
Hello Andrew,
It looks to me as though MED support was not included in your build - look at the libs= line in your code_saturne info . I would expect to see -lmedC in that list of libraries, but I don't see it in yours.
It doesn't appear in your SYRTHES build options either, but I don't think that matters as syrthes doesn't use MED files anyway - the conversion utility is built separately.
Regards,
Brennan
It looks to me as though MED support was not included in your build - look at the libs= line in your code_saturne info . I would expect to see -lmedC in that list of libraries, but I don't see it in yours.
It doesn't appear in your SYRTHES build options either, but I don't think that matters as syrthes doesn't use MED files anyway - the conversion utility is built separately.
Regards,
Brennan
-
Andrew Miner
Re: CS and Syrthes, fresh installation or CAElinux 2010?
Thanks!
It looks like the installation that apt does on Ubuntu 10.10 does not include the MED option. I hoped that this would be the easy way to get it installed.
Would you recommend that I install syrthes and CS from scratch in order to specify options correctly?
My experience:
1. CAELinux 2010 does not have syrthes linked to CS
2. Ubuntu 10.10 and a apt install does not include MED support
Any recommendations on how to get an installation that works? Any good tutorials on the install? I have gotten lost following some postings on the subject.
Thanks
Andy
It looks like the installation that apt does on Ubuntu 10.10 does not include the MED option. I hoped that this would be the easy way to get it installed.
Would you recommend that I install syrthes and CS from scratch in order to specify options correctly?
My experience:
1. CAELinux 2010 does not have syrthes linked to CS
2. Ubuntu 10.10 and a apt install does not include MED support
Any recommendations on how to get an installation that works? Any good tutorials on the install? I have gotten lost following some postings on the subject.
Thanks
Andy
-
Brennan Sharp
Re: CS and Syrthes, fresh installation or CAElinux 2010?
Hello Andy,
Short answer is definitely build your own. Longer answer: Pre-built can be convenient, but you'll get most control over your build if you do it yourself, enabling features you need, omitting those that you don't. Sometimes there's no penalty for building in everything, but building everything can present problems such as some dependencies that just won't build, or aren't compatible with CS or something else that might require them.
I'm running Gentoo, for which everything is typically built from source. In the case of Code Saturne and SYRTHES there's no official package build so I've done my own, but first I made a rough script that sort of streamlines the manual build processes for CS and SYRTHES, so I can offer you yet another set of manual building instructions that may help, or may just add confusion.
From what you've described of the ubuntu situation, I expect you'll be able to make use of some pre-built packages and will have to build a few others manually to fulfill your dependency list. You might even need to build some manually even though there's a pre-built package because sometimes a dependency can be inappropriately configured for code_saturne, as I onec found with MED, although that's no longer the case in that example.
For coupled simulations, I recommend you build and test SYRTHES first as you'll need to configure CS with the path to the SYRTHES installation directory.
If you want to refer to my manual build notes for CS, visit:
http://www.sconegrabber.gen.nz/code_saturne/
I have manual build notes for SYRTHES 3.4.2(5), not yet published, although I see that v3.4.3 has very recently been released and I'm working through the build process for it now. It looks the same so far.
My mistake earlier: the SYRTHES build can theoretically use MED, however I've never been able to build the syrthes2med* utility. I think this is related to a dependency on a much older MED version than is used elsewhere, and something similar has been mentioned in another discussion in this forum. When building SYRTHES, you get by default a syrthes2ensight conversion utility for postprocessing simulation results. I prefer to run Salome for post-processing only because I've already used it for pre-processing, so I use a second conversion of ensight2med, included with Salome (maybe not all versions?). For coupled simulations, viewing Ensight formatted data might be more convenient, with a suitable viewer.
Regards,
Brennan
Short answer is definitely build your own. Longer answer: Pre-built can be convenient, but you'll get most control over your build if you do it yourself, enabling features you need, omitting those that you don't. Sometimes there's no penalty for building in everything, but building everything can present problems such as some dependencies that just won't build, or aren't compatible with CS or something else that might require them.
I'm running Gentoo, for which everything is typically built from source. In the case of Code Saturne and SYRTHES there's no official package build so I've done my own, but first I made a rough script that sort of streamlines the manual build processes for CS and SYRTHES, so I can offer you yet another set of manual building instructions that may help, or may just add confusion.
From what you've described of the ubuntu situation, I expect you'll be able to make use of some pre-built packages and will have to build a few others manually to fulfill your dependency list. You might even need to build some manually even though there's a pre-built package because sometimes a dependency can be inappropriately configured for code_saturne, as I onec found with MED, although that's no longer the case in that example.
For coupled simulations, I recommend you build and test SYRTHES first as you'll need to configure CS with the path to the SYRTHES installation directory.
If you want to refer to my manual build notes for CS, visit:
http://www.sconegrabber.gen.nz/code_saturne/
I have manual build notes for SYRTHES 3.4.2(5), not yet published, although I see that v3.4.3 has very recently been released and I'm working through the build process for it now. It looks the same so far.
My mistake earlier: the SYRTHES build can theoretically use MED, however I've never been able to build the syrthes2med* utility. I think this is related to a dependency on a much older MED version than is used elsewhere, and something similar has been mentioned in another discussion in this forum. When building SYRTHES, you get by default a syrthes2ensight conversion utility for postprocessing simulation results. I prefer to run Salome for post-processing only because I've already used it for pre-processing, so I use a second conversion of ensight2med, included with Salome (maybe not all versions?). For coupled simulations, viewing Ensight formatted data might be more convenient, with a suitable viewer.
Regards,
Brennan