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[foam-extend.org] Installation of foam-extend 3.1 - Packages missing

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Old   October 2, 2015, 03:51
Default Installation of foam-extend 3.1 - Packages missing
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Aude
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Hello everybody,

I'm a newbie to OF, and CFD in general, and I need to work with foam-extend.
I've followed the installation guide on: http://openfoamwiki.net/index.php/In...oam-extend-3.1
And everything seemed to work, but when I type "fe31"
I get the following message:

[lahalle@aglin1 ~]$ fe31
bash: /lahalle/foam/foam-extend-3.1/ThirdParty/packages/openmpi-1.6.5/platforms/linux64GccDPOpt/etc/openmpi-1.6.5.sh: No such file or directory
bash: /lahalle/foam/foam-extend-3.1/ThirdParty/packages/metis-5.1.0/platforms/linux64GccDPOpt/etc/metis-5.1.0.sh: No such file or directory
bash: /lahalle/foam/foam-extend-3.1/ThirdParty/packages/parmetis-4.0.3/platforms/linux64GccDPOpt/etc/parmetis-4.0.3.sh: No such file or directory
bash: /lahalle/foam/foam-extend-3.1/ThirdParty/packages/scotch-6.0.0/platforms/linux64GccDPOpt/etc/scotch-6.0.0.sh: No such file or directory
bash: /lahalle/foam/foam-extend-3.1/ThirdParty/packages/hwloc-1.7.2/platforms/linux64GccDPOpt/etc/hwloc-1.7.2.sh: No such file or directory

I've managed to run some cases without any problem, but I need to run a case in parallel, and if I understood well (correct me if I'm wrong), i need openmpi to run in parallel. So I'm a bit stuck, and puzzled.

Can anybody help me solve this issue? I'm guessing it has something to do with the installation, but I'm not familiar with Linux, and I'm honestly a bit lost, any help would be much appreciated.

Thanks in advance,
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Old   October 3, 2015, 12:17
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Greetings Aude,

We will need a few more details in order to be able to diagnose what went wrong:
  1. Which Linux distribution and version are you using?
  2. Which architecture is your machine is using? In order to find this, run:
    Code:
    uname -m
  3. Please run the following commands:
    Code:
    cd $WM_THIRD_PARTY_DIR
    ./AllMake.pre > ../log.make 2>&1
    cd ..
    ./Allwmake >> log.make 2>&1
    gzip < log.make > log.make.gz
    And attach the file "log.make.gz" in your next post.
Best regards,
Bruno
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Last edited by wyldckat; October 8, 2015 at 17:49. Reason: had placed the 2x "greater than" signs in the wrong line
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Old   October 5, 2015, 03:07
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Hello wyldckat,

Thank you for your reply.
So, regarding the questions you asked me:

1) I'm using Fedora, version 20
2) When I run the command "uname -m" I get the following:
[lahalle@aglin1 ~]$ uname -m
x86_64
3) I attached the log file.

Thanks again for your help, I was getting desperate
Attached Files
File Type: gz log.make.gz (63 Bytes, 5 views)
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Old   October 7, 2015, 09:55
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i have the same problem i tried reinstalling from git and with snapshot; without success.

im using Ubuntu 14.04 the strange think is that is sucessfully compiled fe31 in the past
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Old   October 8, 2015, 18:13
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@Aude:
Quote:
Originally Posted by al0909 View Post
3) I attached the log file.
Unfortunately you did not write the command properly, because the only thing present inside the log file is this:
Code:
bash: /Allwmake: No such file or directory
The correct command starts with a dot "." before the slash "/" :
Code:
./Allwmake >> log.make 2>&1
Please run again the commands I mentioned before:
Code:
cd $WM_THIRD_PARTY_DIR
./AllMake.pre > ../log.make 2>&1
cd ..
./Allwmake >> log.make 2>&1
gzip < log.make > log.make.gz
(Although I did I an error regarding the usage of the "greater than" symbols, but this is now fixed in this post and in the previous post).

_____________

@Henning86: Then please follow the instructions in my question #3 from my previous post, otherwise I can't even start to guess what went wrong .
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Old   October 9, 2015, 05:06
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i use Ubuntu 1404;
uname -m x86_64;


the attached logfile
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File Type: gz log.make.gz (8.6 KB, 3 views)
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Old   October 10, 2015, 09:08
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Hi Henning86,

Well, this is a fairly strange bug. The installation scripts indicate that the 3rd party packages were installed with success, but the necessary shell scripts somehow were not installed.

Please use the following commands:
Code:
cd $WM_THIRD_PARTY_DIR
./AllClean
rm -r platforms
This will clean up the build done in the "ThirdParty" folder.
Next try building everything once again with the commands below. With luck, this will solve the problem:
Code:
./AllMake.pre > ../log.make 2>&1
cd ..
./Allwmake >> log.make 2>&1
gzip < log.make > log.make.gz
If it still has problems, please attach the "log.make.gz" file in you next post.

By the way, which exact origin did your foam-extend 3.1 source code come from?

Best regards,
Bruno
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Old   October 11, 2015, 14:46
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Thanks for the quick reply.



I installed the git versions (with git clone ..) but right now i use the snapshot. But none of them worked.

Best regards

Henning
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Old   October 11, 2015, 14:50
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The log data:
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Old   October 11, 2015, 16:19
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Hi Henning,

Something very strange is going on with your system. But we will have to address one problem at a time.

The first problem is that there are some shell files that are missing and we need to find where they've gone to. To check where they are, please run the following commands:
Code:
foam3rdParty
tar -tf rpmBuild/TGZS/x86_64/openmpi-1.6.5.tgz  > tracking_down.txt
ls -l packages/openmpi-1.6.5/platforms/linux64GccDPOpt/etc  >> tracking_down.txt
find packages/openmpi-1.6.5/platforms/linux64GccDPOpt/  >> tracking_down.txt
gzip < tracking_down.txt > tracking_down.txt.gz
Then please attach the file "tracking_down.txt.gz" in your next post.
The information that is collected with the commands above are for figuring out if the missing files exist in the current installation and in the tarball that the build scripts create.

Essentially I'm looking for these files:
Code:
packages/openmpi-1.6.5/platforms/linux64GccDPOpt/etc/openmpi-default-hostfile
packages/openmpi-1.6.5/platforms/linux64GccDPOpt/etc/openmpi-1.6.5.sh
packages/openmpi-1.6.5/platforms/linux64GccDPOpt/etc/openmpi-1.6.5.csh
packages/openmpi-1.6.5/platforms/linux64GccDPOpt/etc/openmpi-totalview.tcl
packages/openmpi-1.6.5/platforms/linux64GccDPOpt/etc/openmpi-mca-params.conf
where the "openmpi-1.6.5.sh" is the file that is missing.


As for the reason why I commented that your system is doing something strange, is because of this warning message that appears a lot during the build:
Code:
make: Warning: File `Make/linux64GccDPOpt/dontIncludeDeps' has modification time 0,22 s in the future
make: warning:  Clock skew detected.  Your build may be incomplete.
This should not happen. And it doesn't make much sense that a file that was created just now is identified as having been created 0.22s in the future. Is your home folder a mount for a shared folder that is located somewhere else?

Best regards,
Bruno
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Old   October 12, 2015, 04:37
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The folder etc/ and share/ are missing somehow. i tried executing the commands on both servers but the problem is still the same.


Regarding the warning with the future:

We use two servers. One holds all the data and the other one just mounts the data.
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Old   October 12, 2015, 16:53
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Quick answer: A ton of files are missing from the installation folder, but at least the tarball seems to be OK.

Please try the following commands:
Code:
foam3rdParty
for a in rpmBuild/TGZS/x86_64/*.tgz; do tar -xzf $a; done
Make a note if there are any error messages outputted while the second line is running. If a lot of errors occur, then run:
Code:
for a in rpmBuild/TGZS/x86_64/*.tgz; do tar -xzf $a; done > log.tarballs
gzip < log.tarballs > log.tarballs.gz
And attach to the next post the file "log.tarballs.gz".


On the other hand, if there are no error messages, then run:
Code:
source $WM_PROJECT_DIR/etc/bashrc
Does this give you any error messages?
If not, then run:
Code:
foam
./Allwmake > log.make 2>&1
./Allwmake > log.make 2>&1
If all goes well, the content of the file "log.make" should have no error messages... at least I hope so.


Regarding the clocks, please configure your two servers to rely on NTP for clock synchronization, either one syncing with the other, or both syncing with an outside NTP source, because having this time offset might be what's breaking the build system.
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Old   October 13, 2015, 04:16
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Worked no more error messages
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