[sahm]

Hi Everbody
I have a problem that can be easy to solve, But I don't know how.
I wanted to install OpenFoam on a machine with Redhat Enterprise Linux 5, but the Gcc version of Redhat is 4.1.2 which is not good for OpenFOAM 1.6.
The problem is that the wmake is not working, so I have to update GCC version.
I don't have access to the root of Linux, also I can not reinstall it, since there are many other processes running on it. It`s a cluster being used by many people.
The only way I can do is to update GCC for just one single user. But I don't know how. Does anybody know how to update it for just one User?
Any comments is welcome.

[gschaider]

Originally Posted by sahm

Hi Everbody
I have a problem that can be easy to solve, But I don't know how.
I wanted to install OpenFoam on a machine with Redhat Enterprise Linux 5, but the Gcc version of Redhat is 4.1.2 which is not good for OpenFOAM 1.6.
The problem is that the wmake is not working, so I have to update GCC version.
I don't have access to the root of Linux, also I can not reinstall it, since there are many other processes running on it. It`s a cluster being used by many people.
The only way I can do is to update GCC for just one single user. But I don't know how. Does anybody know how to update it for just one User?
Any comments is welcome.

Possible things to look at:
a) have you tried the compiler that comes with the third-party-binaries? (if push comes to shove you can recompile the compiler. There is a script for that in the third-party-directory)
b) there is a project on sourceForge to support OF on CentOS (for all practical purposes CentOS IS RHEL)
c) there is a "technology preview" of gcc44 distributed by RHEL (maybe you can get your admin to install those)

Bernhard

[sahm]

Thank you Bernhard,
Actually the problem is solved now, we contacted the support service for the machine, and we installed the Gcc 4.3.3 rpm file.
But still I would like to know the solution, because this can happen again. I have downloaded the Gcc 4.3.4 on my user from gcc.gnu.org, and unpacked the files, But I don't know how to compile it, can you tell me? Can I compile the Gcc version in the third party of OpenFOAM which doesn't need downloading Gcc again?

[wyldckat]

Greetings SAHM,

Can I compile the Gcc version in the third party of OpenFOAM which doesn't need downloading Gcc again?

There is a script that comes with the ThirdParty General package, named makeGcc. To use it, go to the ThirdParty folder and run:

./makeGcc gcc-4.3.3

This will build the gcc-4.3.3 version that comes with the ThirdParty package.
Now, there are 3 things you'll have to take into account:

1. the ~/OpenFOAM/OpenFOAM-1.6/etc/bashrc script must be executed before running makeGcc.
2. you should only unpack the General packages of OpenFOAM, so it won't trigger the "already built" detection.
3. if your installation is 64bit only, i.e., if the system's gcc isn't built with the multilib option, than my advice is to use the modified script I've already posted some time ago here. Actually, in that thread you'll find a couple more little pearls of wisdom regarding building gcc in OpenFOAM

Additionally, you might need a few more packages to be installed in your Linux installation (local or cluster), that are also listed in that thread above, in post #7. Keep in mind that some of those packages might not be necessary, depending on what you want to built.

I can only assume that if it's in a shared cluster, you won't be needing Paraview on it, but I could be wrong You might actually want Paraview built in the cluster, with the "mesa" driver option on in the makeParaview script, so you can use Paraview's parallel functionality, thus opening the OpenFOAM cases straight from the cluster nodes!

Oh, and just in case you decide to upgrade gcc to 4.4.*, only OpenFOAM 1.6.x is up to specs; the 1.6 version will only build with gcc-4.3.* out-of-the-box.

Best regards,
Bruno

[anfho]

Dear All,
I really appreciate your many comments about OpenFOAM (OF) and gcc. Unfortunately, since I am new to the OF community and not an advanced linux user (I am new to this forum too), I am getting really confused about the OF version that run with wich compiler. Also the cross links make things more difficult for me.

I want to install OF on a cluster with linux red hat enterprise, to which I do not have the root rights. gcc-4.1.2 is pre-installed. I know there is OF 1.7.1 out there wich requires gcc-4.4.4, I believe.

I am really confused what I should do now. Go with an earlier version of OF (the only two I have available are 1.6 and 1.7.0, which don't work with gcc 4.1.2).

Would you recommend to use OF1.6 (32 or 64 bit?) and then upgrade the gcc from the thrid-party package, that comes with the OF downoad package Or would you go with 1.7.1 and try to upgrade the gcc then? Is it really possible to upgrade the gcc compiler on a linux cluster without root rights?

Any help is greatly appreciated.
Best regards,
Andreas

[wyldckat]

Greetings Andreas and welcome to the forum!

I don't know if CentFOAM (official thread http://www.cfd-online.com/Forums/ope...-released.html) has an option to install for user only, but I think that you will need to install some system tools nonetheless, even if you can't upgrade the system's gcc version. And it should work with RHEL!


As for the required gcc version and I quote from the official page:

Originally Posted by http://www.openfoam.com/download/source.php

In particular your system will need to include a recent version of gcc (check with gcc --version, we recommend gcc-4.4.? but gcc-4.3.? is sufficient). If the installed version is not recent source pack for newer versions are available from http://gcc.gnu.org/.

As of OpenFOAM 1.7.1, you can also use gcc 4.5.?.


Now, as for building a custom non system installed gcc: You can get the gcc 4.3.3 version that comes with OpenFOAM 1.6, available here. You can use its pre-built gcc version that comes with the binaries. But if you want to build that version from scratch... er, my previous post explains about that


Or, if you feel like experimenting, you could try using FreeFOAM (it's OpenFOAM, but it uses cmake), which the latest git version apparently allows building OpenFOAM with gcc 4.1.2

Best regards,
Bruno

[anfho]

Hi Bruno,
thanks a lot for the quick reply. I think the best way for me is to go with OF-1.7.1 and install the gcc-4.3.3 that comes with the OF-1.6 package. What did you mean with building from scratch? I am sure there is a thread that explains how to install gcc-4.4.4 from OF-1.6 and I do not want to kill too much of your time, however, since there are a lot of details that have to be changed in the source files, I would appreciate if we could go through that step by step. So the best bet is to start with your reply from above? Thanks!
Andreas

[wyldckat]

Hi Andreas,

What I meant with «building from scratch» is to build gcc 4.3.3 that comes with ThirdParty-1.6.General, instead of using the pre-built version that comes with the binary ThirdParty-1.6.linux(64)Gcc package.

I suggest that you first try CentFOAM (see this thread: http://www.cfd-online.com/Forums/ope...-released.html). If that doesn't work, then I can try writing something more dedicated to this issue. Actually, I can even modify a script I've already got for cross-compiling gcc with mingw... but like I said, only after you've tried CentFOAM

Best regards,
Bruno

[anfho]

Bruno,
not sure what SL 5.x stands for. Is that the RHEL version? The RHEL version on the cluster that I am using is 4.1.2-46. Can I install the release you are referencing to in that OS?
Andreas

[wyldckat]

Hi Andreas,

I believe SL is Scientific Linux. Those three versions are all related to Red Hat Enterprise Linux (i.e., RHEL ).

Unfortunately, I believe that CentFOAM only targets the 5.x series

Later today I'll try to either explain things better or modify the script I have

Best regards,
Bruno

[anfho]

Bruno,
also: installing CentFOAM requires the "yum" command, which needs root rights. Since I do not have root rights, I think installing CentFOAM is not really an option... So installing OF1.7.1 with gcc4.3.3 rom OF1.6 anyway?
Andreas

[wyldckat]

Greetings Andreas,

EDIT: I've made a blog post with an update of this build-gcc44 script, as well with build-gcc45: Automated scripts for building gcc 4.4.x and 4.5.x for using with OpenFOAM 1.7 series

OK, I've created a modified version of the build-mingw44 script I made at blueCAPE for cross-compiling OpenFOAM 1.7.0 in Linux for Windows (see here if you're curious). The resulting script is named build-gcc44, which will take care of downloading and building binutils and gcc and some of it's direct dependencies (namely gmp and mpfr). Keep in mind that this script will not take care of all of the necessary steps to get your system ready for building OpenFOAM!

The following steps are needed for this to work (might not be complete, since I haven't tested this yet on a CentOS 4):

1. Check and/or request your cluster/RHEL administrator to install these packages (the names are from Debian, so you'll need to find similar names in RHEL):
   • flex - it should include the binaries flex and flex++, as well as FlexLexer.h.
   • libreadline5-dev - this has the readline library and respective header files.
     
   • texinfo - this is required during building gcc for documentation... but I can't remember what were the needed files
   • byacc and bison - these are two applications, one needed for building gcc, the other for building OpenFOAM.
2. Get OpenFOAM 1.7.0/1 or 1.7.x into your system, by following the instructions at www.openfoam.com.
3. After getting OpenFOAM's bashrc sourced (search for «source the etc/bashrc» in the project's installation page) into the working environment, edit the file "$WM_PROJECT_DIR/etc/settings.sh" and change the following lines:
   • change:

     gcc_version=gcc-4.4.3

     to:

     gcc_version=gcc-4.4.4

   • change:

     : ${compilerInstall:=system}

     to:

     : ${compilerInstall:=OpenFOAM}

4. Source the bashrc file once more, or start a new terminal and source it again.
5. Download the attached build-gcc44.tar.gz and unpack it in the "$WM_THIRD_PARTY_DIR".
6. Now run:

   cd $WM_THIRD_PARTY_DIR
   ./build-gcc44

   It will download the files mentioned before (binutils, gcc, gmp, mpfr) and build them in the proper order.
7. Whenever there is an error, it will tell you in which log file the error is listed. Check it for the things it says it needs and try to get them. If you can't figure it out, compress and attach the relevant log file.
   If you can get them, then run build-gcc44 again.
8. When you finally have gcc fully built, then you can move on to building OpenFOAM.

Now, keep in mind that these steps will only get as far as building OpenFOAM and OpenMPI. And this is assuming that you can get the remaining necessary packages that I'm not giving instructions about. If you need a software package that you can't request to be installed in the system, then you will have to download the source code and build it yourself... usually with a group of commands like this:

./config --prefix=/the/folder/where/to/install
make
make install

As for ParaView, it requires a larger heap load of packages to be installed and/or built (most likely all would have to be built in RHEL 4 ) which is too much work to even bother, or so I believe The best option would be to simply get the ready to use version from www.paraview.org and follow the instructions I've already detailed here: Using the official pre-built ParaView 3.8.0 version with OpenFOAM...

Good luck!
Bruno

[anfho]

Hi Bruno,
thanks a lot for your post. I really appreciate your help. Finally, I could also get a hold of the cluster admin. And I have to apologize as I am a new user of this cluster, too. The admin told me that there was CentOS 5.4 installed. Is this the same as CentOS/SL 5.x? I got confused about the Linux versions. Because when I entered "gcc --version" I got the output: "gcc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-46) Copyright (C) 2006 Free Software Foundation, Inc." Therefore I thought RHEL 4.1.2 would be installed.
But still - eventhough CentOS 5.4 is installed it is the old gcc 4.1.2 compiler. So is it possible to use CentFOAM (as disussed here: http://www.cfd-online.com/Forums/ope...eleased-2.html) and then try to find a work around of the "yum" command? Meaning can I update the gcc compiler on CentOS 5.x also, like you showed me for RHEL 4.x above?

Also, why does OpenCFD and everyone in this forum recommend to compile OpenFOAM with gcc? gcc is known to produce inefficient codes (at least that what the cluster admin says). Wouldn't it be better to use icc or pgi? On the cluster there is icc 10.1 installed.

As far as the needed packages for gcc go:
-flex version 2.5.4
-bison 2.3
is installed. I am not sure about
-libreadlines5-dev
-texinfo
-byacc
are these standard packages? Are they at least standard and included in CentOS 5.4?

Thanks very much!
Andreas

[anfho]

Is there a command to check the linux version?

[wyldckat]

Hi Andreas,

Posting the same thing on two "similar" threads brings people to a paradoxal issue: "to which thread do we answer" and you will probably lead different people to answer you pretty much the same thing!

So, let's go through your question list, one issue at a time:

• Since you do have access to CentOS 5.4 (and yes, it is considered CentOS 5.x, since "x=0:5" ), then ask your system's admin to either check or install the packages listed on Linnemann's CentFOAM page under manual installation, namely the packages:

  ncurses-devel tix.x86_64 glibc-devel flex-devel zlib-devel libXt-devel

  The remaining ones I believe that by your description you already have access to. Then you can either use Linnemann's script for finishing the installation, or you can continue to follow the "manual installation" instructions. AFAIK, CentFOAM's packages of OpenFOAM 1.7.0 already come with gcc 4.4.4 pre-built and ready to use, so you will not have to suffer the small hell of building gcc
• As for ICC or PGI: Intel's C/C++ compiler is roughly supported in OpenFOAM. In my signature link you can find a link to a thread that tells you what is missing in OpenFOAM for it to build with ICC. But I'm not sure what is the lowest ICC version compatible with OpenFOAM 1.7.
• As for ICC being better than GCC: well, OpenFOAM is open source code and GCC is also open source, sooo it's only natural that OpenFOAM sticks with open source software Additionally, Intel's C/C++ compiler has had it's problems with the CFD crowd, because although ICC provides faster applications, it sometimes looses floating point accuracy in favor of speed.
  So, what basically happens is that when a CFD code is developed with a specific compiler version, the resulting built applications are validated with experimental data or previously known solutions. So, if OpenFOAM is well tested with GCC, and builds with ICC, it doesn't necessarily mean that the results with ICC will be as valid as the results with GCC!
• As for knowing the Linux version, there are several ways of knowing, such as:

  Originally Posted by http://www.howtoforge.com/how_to_find_out_about_your_linux_distribution

  cat /etc/issue
  cat /etc/*release
  cat /etc/*version

• Last but not least, the script build-gcc44 I've posted yesterday does automatically what Linnemann's link for gcc 4.3.x explains.

Best regards,
Bruno

PS: By the way, this forum allows you to edit your posts, so you didn't have to do two consecutive posts on the same thread

[anfho]

Hi Bruno,
again, thanks very much for the great help. I am working with the cluster admin on these issues now and will get back to you when I (we) encounter difficulties. Just one question in the meantime: Is is possible to upgrade to newer versions once I get CentFOAM to work? The newest OF release is 1.7.1 (as on: http://www.openfoam.com/download/source.php) and CentFOAM is basically OF 1.7.0, right?
Best regards, Andreas

[wyldckat]

Hi Andreas,

It's pretty easy to have 1.7.1 and 1.7.x once you've got OpenFOAM 1.7.0 up and running. Simply run:

cd $WM_THIRD_PARTY/../
ln -s ThirdParty-1.7.0 ThirdParty-1.7.1
ln -s ThirdParty-1.7.0 ThirdParty-1.7.x

Then unpack OpenFOAM-1.7.1.gtgz or use git to get 1.7.x. Then in the end of your "~/.bashrc" file, do something like this:

alias of170='. $HOME/OpenFOAM/OpenFOAM-1.7.0/etc/bashrc'
alias of171='. $HOME/OpenFOAM/OpenFOAM-1.7.1/etc/bashrc
alias of17x='. $HOME/OpenFOAM/OpenFOAM-1.7.x/etc/bashrc

Then every time you start a new terminal, run of170 or of171 or of17x and you will have the desired environment set to go.

Finally, run Allwmake in OpenFOAM-1.7.1 or 1.7.x. And voilá, if all goes well, you are ready to go!

Best regards,
Bruno

[pit]

Hi Bruno,
I found this thread because I want reply the CentFOAM thread. Here I've installed CentFOAM (OF-1.7.0) on a RHEL 5 machine after a lot of problems trying to install OF on the normal way.

First it looks quite good and I have no critical errors after the 'foamInstallationTest'. Also it runs with the standard solver etc.
But now I tried to compile extensions/solver with wmake. I get no errors while compiling, but when using it leads to segfault.

[msuho]

Hi. Hope this thread is still active.

I'm trying to install OpenFOAM 1.7.1 on RHEL 5.4 by building from source. The gcc-4.4.4 compiler is installed on this system under /opt, as it is a cluster system with many users, and all additions to the red hat binary software stack are built as modules. I can build the source as per the download instructions, & run the installation test successfully, but when I proceed with trying the tutorials, I find that
I am not linking to the proper libstd++.so.6. My LD_LIBRARY_PATH lists the gcc-4.4.4 lib path first, but no dice.

For instance, for icoFoam I show:

: ldd icoFoam
./icoFoam: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by ./icoFoam)
./icoFoam: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by ./icoFoam)
./icoFoam: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /opt/crc/OpenFOAM/1.7.1/gcc-4.4.4/OpenFOAM-1.7.1/lib/linux64GccDPOpt/libfiniteVolume.so)
./icoFoam: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by /opt/crc/OpenFOAM/1.7.1/gcc-4.4.4/OpenFOAM-1.7.1/lib/linux64GccDPOpt/libfiniteVolume.so)
./icoFoam: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /opt/crc/OpenFOAM/1.7.1/gcc-4.4.4/OpenFOAM-1.7.1/lib/linux64GccDPOpt/libOpenFOAM.so)
./icoFoam: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by /opt/crc/OpenFOAM/1.7.1/gcc-4.4.4/OpenFOAM-1.7.1/lib/linux64GccDPOpt/libOpenFOAM.so)
./icoFoam: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by /opt/crc/OpenFOAM/1.7.1/gcc-4.4.4/OpenFOAM-1.7.1/lib/linux64GccDPOpt/libtriSurface.so)
./icoFoam: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /opt/crc/OpenFOAM/1.7.1/gcc-4.4.4/OpenFOAM-1.7.1/lib/linux64GccDPOpt/libtriSurface.so)
./icoFoam: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by /opt/crc/OpenFOAM/1.7.1/gcc-4.4.4/OpenFOAM-1.7.1/lib/linux64GccDPOpt/libmeshTools.so)
./icoFoam: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /opt/crc/OpenFOAM/1.7.1/gcc-4.4.4/OpenFOAM-1.7.1/lib/linux64GccDPOpt/libmeshTools.so)
./icoFoam: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by /opt/crc/OpenFOAM/1.7.1/gcc-4.4.4/OpenFOAM-1.7.1/lib/linux64GccDPOpt/libdecompositionMethods.so)
./icoFoam: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /opt/crc/OpenFOAM/1.7.1/gcc-4.4.4/OpenFOAM-1.7.1/lib/linux64GccDPOpt/libdecompositionMethods.so)
./icoFoam: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by /opt/crc/OpenFOAM/1.7.1/gcc-4.4.4/OpenFOAM-1.7.1/lib/linux64GccDPOpt/liblagrangian.so)
./icoFoam: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /opt/crc/OpenFOAM/1.7.1/gcc-4.4.4/OpenFOAM-1.7.1/lib/linux64GccDPOpt/liblagrangian.so)
libfiniteVolume.so => /opt/crc/OpenFOAM/1.7.1/gcc-4.4.4/OpenFOAM-1.7.1/lib/linux64GccDPOpt/libfiniteVolume.so (0x00002b1e23ada000)
libOpenFOAM.so => /opt/crc/OpenFOAM/1.7.1/gcc-4.4.4/OpenFOAM-1.7.1/lib/linux64GccDPOpt/libOpenFOAM.so (0x00002b1e24a2d000)
libdl.so.2 => /lib64/libdl.so.2 (0x0000003dbf400000)
libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x0000003dc5000000)
libm.so.6 => /lib64/libm.so.6 (0x0000003dbf000000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x0000003dc4000000)
libc.so.6 => /lib64/libc.so.6 (0x0000003dbec00000)
libPstream.so => /opt/crc/OpenFOAM/1.7.1/gcc-4.4.4/OpenFOAM-1.7.1/lib/linux64GccDPOpt/dummy/libPstream.so (0x00002b1e2506b000)
libtriSurface.so => /opt/crc/OpenFOAM/1.7.1/gcc-4.4.4/OpenFOAM-1.7.1/lib/linux64GccDPOpt/libtriSurface.so (0x00002b1e2526f000)
libmeshTools.so => /opt/crc/OpenFOAM/1.7.1/gcc-4.4.4/OpenFOAM-1.7.1/lib/linux64GccDPOpt/libmeshTools.so (0x00002b1e254e1000)
libz.so.1 => /usr/lib64/libz.so.1 (0x0000003dbfc00000)
/lib64/ld-linux-x86-64.so.2 (0x0000003dbe800000)
libdecompositionMethods.so => /opt/crc/OpenFOAM/1.7.1/gcc-4.4.4/OpenFOAM-1.7.1/lib/linux64GccDPOpt/libdecompositionMethods.so (0x00002b1e25940000)
liblagrangian.so => /opt/crc/OpenFOAM/1.7.1/gcc-4.4.4/OpenFOAM-1.7.1/lib/linux64GccDPOpt/liblagrangian.so (0x00002b1e25b5f000)
libscotchDecomp.so => /opt/crc/OpenFOAM/1.7.1/gcc-4.4.4/OpenFOAM-1.7.1/lib/linux64GccDPOpt/dummy/libscotchDecomp.so (0x00002b1e25d7a000)
libmetisDecomp.so => /opt/crc/OpenFOAM/1.7.1/gcc-4.4.4/OpenFOAM-1.7.1/lib/linux64GccDPOpt/dummy/libmetisDecomp.so (0x00002b1e25f7f000)
libparMetisDecomp.so => /opt/crc/OpenFOAM/1.7.1/gcc-4.4.4/OpenFOAM-1.7.1/lib/linux64GccDPOpt/dummy/libparMetisDecomp.so (0x00002b1e26183000)
newcell.crc.nd.edu{msuhovec}83:

I am not familiar with wmake- I can't figure out where the library paths are being set during the build.

I've totally blown away the source tree & rebuilt it twice to make sure I was not picking up anything built with gcc 4.1.2, but I've gotten the same results.

Any ideas appreciated.

Thanks,

Mark

[wyldckat]

Greetings Mark and welcome to the forum!

You seem to have root powers, so why don't you try CentFOAM: http://www.cfd-online.com/Forums/ope...-released.html

It has instructions for both automatic and manual installations of OpenFOAM for CentOS, RHEL and SL 5.x. And I believe it has already been updated to 1.7.1. If not, once you have 1.7.0 working, it'll be very easy to get the 1.7.1 working!

Only if CentFOAM goes wrong for you, then we can try and help you

Best regards,
Bruno