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[OpenFOAM.org] Problems installing OpenFOAM 2.3.0 on CentOS-6.6-x86-64

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Old   November 22, 2015, 16:12
Default Problems installing OpenFOAM 2.3.0 on CentOS-6.6-x86-64
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Milan Šekularac
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I followed the instructions on https://openfoamwiki.net/index.php/I...CentOS_SL_RHEL

...for the CentOS 6.5 (mine is 6.6 if relevant). Hopefully I did it properly but here is the problem:

I was about to try the tutorials (cavity flow) and when I type the blockMesh command:

> blockMesh. Gives and error message: bash: blockMesh: command not found

and when I type the full pathname: > ~/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64Gcc48DPOpt/bin/blockMesh


there is an error message: /home/username/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64Gcc48DPOpt/bin/blockMesh: error while loading shared libraries: libblockMesh.so: cannot open shared object file: No such file or directory


Then I followed the advice of an experienced user given bellow, but that did not solve the issue either. Maybe I should remove and reinstall OpenFoam again.


# last tip I tried:
Your library has either failed to compile, or you are trying to execute the solver without sourcing the global /etc/bashrc configuration script.
Execute
. ~/OpenFOAM/OpenFOAM-2.3.0/etc/bashrc
in the terminal where you are trying to use blockMesh. Execute blockMesh again.
If that failed, try to compile the libraries by executing cd $FOAM_SRC , then executing ./Allwmake. Once the build has finished Execute Allwmake in $FOAM_SRC again and observe the output: you should see a bunch of lines stating that different libraries are "up to date" . You should see no errors there.

Received the "up to date" but also error messages. Hopefully you can give me a hand here.
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Old   November 22, 2015, 16:29
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I repeated some of the installation steps again, went back to tutorials directory, and the blockMesh seems to be working now...

Here's the output text it generated in the command line, upon execution (cavity flow tutorial case):

0 constant system
[username@localhost cavity]$
[username@localhost cavity]$
[username@localhost cavity]$ blockMesh
/*---------------------------------------------------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 2.3.0 |
| \\ / A nd | Web: www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
Build : 2.3.0-f5222ca19ce6
Exec : blockMesh
Date : Nov 22 2015
Time : 23:23:37
Host : "localhost.localdomain"
PID : 15508
Case : /home/username/OpenFOAM/username-2.3.0/run/tutorials/incompressible/icoFoam/cavity
nProcs : 1
sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE).
fileModificationChecking : Monitoring run-time modified files using timeStampMaster
allowSystemOperations : Disallowing user-supplied system call operations

// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Create time

Creating block mesh from
"/home/username/OpenFOAM/username-2.3.0/run/tutorials/incompressible/icoFoam/cavity/constant/polyMesh/blockMeshDict"
Creating curved edges
Creating topology blocks
Creating topology patches

Creating block mesh topology

Check topology

Basic statistics
Number of internal faces : 0
Number of boundary faces : 6
Number of defined boundary faces : 6
Number of undefined boundary faces : 0
Checking patch -> block consistency

Creating block offsets
Creating merge list .

Creating polyMesh from blockMesh
Creating patches
Creating cells
Creating points with scale 0.1
Block 0 cell size :
i : 0.005 .. 0.005
j : 0.005 .. 0.005
k : 0.01 .. 0.01


Writing polyMesh
----------------
Mesh Information
----------------
boundingBox: (0 0 0) (0.1 0.1 0.01)
nPoints: 882
nCells: 400
nFaces: 1640
nInternalFaces: 760
----------------
Patches
----------------
patch 0 (start: 760 size: 20) name: movingWall
patch 1 (start: 780 size: 60) name: fixedWalls
patch 2 (start: 840 size: 800) name: frontAndBack

End
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Old   November 22, 2015, 16:32
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Quick answer: If you still have problems with your installation, please follow the instructions given in step #15.
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Old   November 22, 2015, 16:43
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Thanks! This is what I get @ step 15:

[username@localhost cavity]$ icoFoam -help

Usage: icoFoam [OPTIONS]
options:
-case <dir> specify alternate case directory, default is the cwd
-noFunctionObjects
do not execute functionObjects
-parallel run in parallel
-roots <(dir1 .. dirN)>
slave root directories for distributed running
-srcDoc display source code in browser
-doc display application documentation in browser
-help print the usage

Using: OpenFOAM-2.3.0 (see www.OpenFOAM.org)
Build: 2.3.0-f5222ca19ce6
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Old   November 23, 2015, 12:18
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I am having this issue trying to run Para View:

[username@localhost PV4Readers]$ paraFoam

FATAL ERROR: ParaView reader module libraries do not exist

Please build the reader module before continuing:
cd $FOAM_UTILITIES/postProcessing/graphics/PV4Readers
./Allwclean
./Allwmake
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Old   November 23, 2015, 15:22
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Hi Milan,

I've got the feeling that you're reading the instructions at a very high speed
I say this because the step #15 has 4 sub-steps and you only did the first sub-step.

As for the latest issue, the fix should be just a matter of doing the commands the paraFoam script told you to do, namely:
Code:
cd $FOAM_UTILITIES/postProcessing/graphics/PV4Readers 
wmSET $FOAM_SETTINGS
./Allwclean 
./Allwmake
If this doesn't work, then please run the following commands:
Code:
cd $WM_PROJECT_DIR
./Allwmake > make.log 2>&1
gzip < make.log > make.log.gz

pwd
And then attach the file "make.log.gz" to your next post.
If you don't know where the file is located, the last command will have told the full folder path inside which the file is located.

Best regards,
Bruno

---------------

Sorry, I only saw just now what you wrote me via PM:
Quote:
Originally Posted by Milan2013
Afer I do as it is written above, it appears:
[username@localhost PV4Readers]$ ./Allwmake
ERROR: ParaView not found in /home/username/OpenFOAM/ThirdParty-2.3.0/platforms/linux64Gcc48/ParaView-4.1.0

This is what I have in the PV4Readers dir:
[username@localhost PV4Readers]$ ls
Allwclean Allwmake log.make log.makePV PV4blockMeshReader PV4FoamReader vtkPV4Readers

while in the directory: /home/username/OpenFOAM/ThirdParty-2.3.0/platforms/linux64Gcc48/

..I have the:
boost_1_54_0 CGAL-4.3 cmake-2.8.12.1 paraview-4.1.0 qt-4.8.4 scotch_6.0.0
OK, this is an old bug that I never managed to figure out what it really was.

I've taken a better look at the code and I believe the following commands will help solve the problem:
Code:
foam
sed -i -e 's/#\(export ParaView_VERSION=4.1.0\)/\1/' etc/config/paraview.sh

foam3rdParty
mv platforms/linux64Gcc48/paraview-4.1.0 platforms/linux64Gcc48/ParaView-4.1.0

wmSET $FOAM_SETTINGS
which paraview
If all goes well, the last command should tell you that "paraview" is located at "platforms/linux64Gcc48/ParaView-4.1.0". Then you can do again:
Code:
cd $FOAM_UTILITIES/postProcessing/graphics/PV4Readers 
wmSET $FOAM_SETTINGS
./Allwclean 
./Allwmake
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Old   November 24, 2015, 03:11
Default make.log.gz
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here's the make.log.gz after the first part of the instructions above
Attached Files
File Type: gz make.log.gz (5.4 KB, 1 views)
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Old   November 24, 2015, 03:28
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The first segment returns this in the command line:

[username@localhost ThirdParty-2.3.0]$ mv platforms/linux64Gcc48/paraview-4.1.0 platforms/linux64Gcc48/ParaView-4.1.0
mv: cannot stat `platforms/linux64Gcc48/paraview-4.1.0': No such file or directory
[username@localhost ThirdParty-2.3.0]$
[username@localhost ThirdParty-2.3.0]$ wmSET $FOAM_SETTINGS
[username@localhost ThirdParty-2.3.0]$ which paraview
/usr/bin/which: no paraview in (/home/username/OpenFOAM/ThirdParty-2.3.0/platforms/linux64Gcc48/gperftools-svn/bin:/home/username/OpenFOAM/ThirdParty-2.3.0/platforms/linux64Gcc48/ParaView-4.1.0/bin:/home/username/OpenFOAM/ThirdParty-2.3.0/platforms/linux64Gcc48/cmake-2.8.12.1/bin:/home/username/OpenFOAM/ThirdParty-2.3.0/platforms/linux64/gcc-4.8.1/bin:/home/username/OpenFOAM/username-2.3.0/platforms/linux64Gcc48DPOpt/bin:/home/username/OpenFOAM/site/2.3.0/platforms/linux64Gcc48DPOpt/bin:/home/username/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64Gcc48DPOpt/bin:/home/username/OpenFOAM/OpenFOAM-2.3.0/bin:/home/username/OpenFOAM/OpenFOAM-2.3.0/wmake:/usr/lib64/openmpi/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/username/bin)


...while the second segments returns:
[username@localhost PV4Readers]$ cd $FOAM_UTILITIES/postProcessing/graphics/PV4Readers
[username@localhost PV4Readers]$ wmSET $FOAM_SETTINGS
[username@localhost PV4Readers]$ ./Allwclean
+ wclean libso vtkPV4Readers
wclean vtkPV4Readers
+ PV4blockMeshReader/Allwclean
+ rm -f '/home/username/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64Gcc48DPOpt/lib/libPV4blockMeshReader*'
+ rm -rf PV4blockMeshReader/Make
+ wclean libso vtkPV4blockMesh
wclean vtkPV4blockMesh
+ PV4FoamReader/Allwclean
+ rm -f '/home/username/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64Gcc48DPOpt/lib/libPV4FoamReader*'
+ rm -rf PV4FoamReader/Make
+ wclean libso vtkPV4Foam
wclean vtkPV4Foam
[username@localhost PV4Readers]$ ./Allwmake
ERROR: ParaView not found in /home/username/OpenFOAM/ThirdParty-2.3.0/platforms/linux64Gcc48/ParaView-4.1.0

Indeed there is no ParaView-4.1.0 in the last directory:
[username@localhost PV4Readers]$ pwd
/home/username/OpenFOAM/OpenFOAM-2.3.0/applications/utilities/postProcessing/graphics/PV4Readers
[username@localhost PV4Readers]$ ls
Allwclean Allwmake log.make log.makePV PV4blockMeshReader PV4FoamReader vtkPV4Readers


what do you recommend me to do?
Thanks
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Old   November 24, 2015, 04:06
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PS. Looks like the make command is missing the path, it returns there is no ParaView-4.1.0 in the path: [username@localhost PV4Readers]$ ./Allwmake
ERROR: ParaView not found in /home/username/OpenFOAM/ThirdParty-2.3.0/platforms/linux64Gcc48/ParaView-4.1.0

...well there it is not - because it the proper path is one up, at:
/home/username/OpenFOAM/ThirdParty-2.3.0/platforms/linux64Gcc48

[username@localhost linux64Gcc48]$ cd /home/username/OpenFOAM/ThirdParty-2.3.0/platforms/linux64Gcc48
[username@localhost linux64Gcc48]$ ls
boost_1_54_0 CGAL-4.3 cmake-2.8.12.1 ParaView-4.1.0 qt-4.8.4 scotch_6.0.0
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Old   November 24, 2015, 14:51
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Hi Milan,

Sorry, but I wasn't able to answer during the day.

Something really strange is going on with your installation of ParaView.
The good news is that the "make.log" file tells us that everything has been built with success, therefore OpenFOAM is ready to be used.

As for ParaView, please do the following commands:
Code:
foam3rdParty
./makeParaView4 -qmake $WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/qt-4.8.4/bin/qmake -mpi -python > log.makePV 2>&1
gzip < log.makePV > log.makePV.gz

pwd
This essentially will rebuild ParaView 4.1.0 again. Then please attach in your next post the file "log.makePV.gz" that is located in the folder that is pointed out by the last command, because this log file will tell us if anything goes wrong during the build.

With any luck, then try again:
Code:
cd $FOAM_UTILITIES/postProcessing/graphics/PV4Readers 
wmSET $FOAM_SETTINGS

which paraview

./Allwclean 
./Allwmake
The "which" command should hopefully finally find where ParaView is installed. If it doesn't, then the "log.makePV" file will tell us what's going on.

Best regards,
Bruno
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Old   November 25, 2015, 12:12
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Thank you for the support.
Well, I did as you wrote above. Bellow is the log.makePV.gz file.

After running the second part I get something like before:


[username@localhost PV4Readers]$ cd $FOAM_UTILITIES/postProcessing/graphics/PV4Readers
[username@localhost PV4Readers]$ wmSET $FOAM_SETTINGS
[username@localhost PV4Readers]$
[username@localhost PV4Readers]$ which paraview
~/build/paraview/bin/paraview
[username@localhost PV4Readers]$
[username@localhost PV4Readers]$ ./Allwclean
+ wclean libso vtkPV4Readers
wclean vtkPV4Readers
+ PV4blockMeshReader/Allwclean
+ rm -f '/home/username/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64Gcc48DPOpt/lib/libPV4blockMeshReader*'
+ rm -rf PV4blockMeshReader/Make
+ wclean libso vtkPV4blockMesh
wclean vtkPV4blockMesh
+ PV4FoamReader/Allwclean
+ rm -f '/home/username/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64Gcc48DPOpt/lib/libPV4FoamReader*'
+ rm -rf PV4FoamReader/Make
+ wclean libso vtkPV4Foam
wclean vtkPV4Foam
[username@localhost PV4Readers]$ ./Allwmake
ERROR: ParaView not found in /home/username/OpenFOAM/ThirdParty-2.3.0/platforms/linux64Gcc48/ParaView-4.1.0

Last night I followed another advice I received, to download the paraview binaries. Here it is:
,,Get the paraview binaries: http://www.paraview.org/download/
Download the linux 64 or 32 bit binary (depending on your OS installation), save it somewhere in your home folder, e.g. ~/build/, unpack it, rename the folder to ~/build/paraview and extend the PATH
export PATH=~/build/paraview/bin:$
PATH
in ~/.bashrc.
That's it. You con't have to compile paraview or install it any other way. I'm using Arch Linux and the binary is working fine.''


I did so, and now I can run the paraview (say tutorial case cavity)by typing:
touch $FOAM_RUN/tutorials/incompressible/icoFoam/cavity/case.foam
paraview $FOAM
_RUN/tutorials/incompressible/icoFoam/cavity/case.foam


The which command above indeed returns:
[username@localhost PV4Readers]$ which paraview
~/build/paraview/bin/paraview

Would be nice to resolve the "ParaFoam" compilation problem above though, since I plan to use this OS further on another computer....just to have the same OS as on a powerful cluster which will be available to me from time to time, where the CentOS 6.6 and OF 2.3 are installed currently.
Sorry for taking your time,
Milan
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Old   November 25, 2015, 12:14
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the log.makePV.gz
Attached Files
File Type: gz log.makePV.gz (154.8 KB, 2 views)
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Old   November 26, 2015, 02:15
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Hi Milan,

If you have a pre-built installation, you can try using:
Code:
paraFoam -builtin
and it should launch ParaView without the need for the official plug-in (PV4Readers).

As for the custom installation, I've examined the "log.makePV.gz" and it only fails when it reaches the installation step, with the following message:
Code:
Install the project...
-- Install configuration: "Release"
CMake Error at cmake_install.cmake:36 (FILE):
  file cannot create directory:
  /home/username/OpenFOAM/ThirdParty-2.3.0/platforms/linux64Gcc48/ParaView-4.1.0/share/paraview-4.1.
  Maybe need administrative privileges.


make: *** [install] Error 1
    ---
    Installation complete for paraview-4.1.0
    Set environment variables:

        export ParaView_DIR=/home/username/OpenFOAM/ThirdParty-2.3.0/platforms/linux64Gcc48/ParaView-4.1.0
        export PATH=$ParaView_DIR/bin:$PATH
        export PV_PLUGIN_PATH=$FOAM_LIBBIN/paraview-4.1
    ---

Done
Therefore, please try the following commands:
Code:
foam3rdParty
rm -r platforms/linux64Gcc48/ParaView-4.1.0/

./makeParaView4 -no-config -no-make -qmake $WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/qt-4.8.4/bin/qmake -mpi -python > log.makePV2 2>&1
gzip < log.makePV2 > log.makePV2.gz

pwd
What's done above is to eliminate the previous installation that failed and then it runs the script with the options to not do the config and make steps, therefore doing only the final installation step.
Then take a look at the lines I mentioned above from "log.makePV" and compare with what you now get in "log.makePV2". If you can't figure out what the problem is, please attach the file "log.makePV2.gz".

Best regards,
Bruno

edit: sorry, wrote this post in a hurry, hope to not have missed any important detail...

Last edited by wyldckat; November 26, 2015 at 02:16. Reason: see "edit:"
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Old   November 26, 2015, 05:33
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Thanks!
Here is what is written at the bottom of the log.makePV2


[100%] Built target paraview
[100%] Built target paraview-launcher
Install the project...
-- Install configuration: "Release"
CMake Error at cmake_install.cmake:36 (FILE):
file cannot create directory:
/home/username/OpenFOAM/ThirdParty-2.3.0/platforms/linux64Gcc48/ParaView-4.1.0/share/paraview-4.1.
Maybe need administrative privileges.


make: *** [install] Error 1
---
Installation complete for paraview-4.1.0
Set environment variables:

export ParaView_DIR=/home/username/OpenFOAM/ThirdParty-2.3.0/platforms/linux64Gcc48/ParaView-4.1.0
export PATH=$ParaView_DIR/bin:$PATH
export PV_PLUGIN_PATH=$FOAM_LIBBIN/paraview-4.1
---

Done


Should I run this as administrator?
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Old   November 26, 2015, 05:35
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the log.makePV2.gz
Attached Files
File Type: gz log.makePV2.gz (3.9 KB, 2 views)
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Old   November 27, 2015, 03:53
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Hi Milan,

Building as root (admin) is unlikely to solve the problem. It might have been the origin of the problem in the first place.

Please do the following commands:
Code:
foam3rdParty
ls -l platforms/linux64Gcc48/ > filelist.txt
ls -l platforms/linux64Gcc48/ParaView-4.1.0 >> filelist.txt
ls -l platforms/linux64Gcc48/ParaView-4.1.0/share >> filelist.txt

gzip < build/linux64Gcc48/ParaView-4.1.0/cmake_install.cmake  > paraview410.cmake_install.cmake.gz
gzip < filelist.txt > filelist.txt.gz

pwd
Then please attach the files "paraview410.cmake_install.cmake.gz" and "filelist.txt.gz". Hopefully this will give me enough information to diagnose the problem.
The "ls -l" commands will tell us who created the original folders and their permissions. The "cmake_install.cmake" will tell us if the file is corrupted.

Best regards,
Bruno
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Old   November 28, 2015, 11:59
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Thanks!!!
here they are
Attached Files
File Type: gz filelist.txt.gz (208 Bytes, 1 views)
File Type: gz paraview410.cmake_install.cmake.gz (1.4 KB, 1 views)
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Old   November 28, 2015, 12:24
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Hi Milan,

Interesting, seems that somehow "platforms/linux64Gcc48/ParaView-4.1.0" is a file instead of a folder... which I didn't expected in the instructions I gae before . But at least the "cmake_install.cmake" file seems OK.

Please run these commands:
Code:
foam3rdParty
rm platforms/linux64Gcc48/ParaView-4.1.0
ls -l platforms/linux64Gcc48/ParaView-4.1.0
Does the second command give any error message? And what does the third command give you?

If the second command tells you the path/file/folder doesn't exist, then run:
Code:
./makeParaView4 -no-config -no-make -qmake $WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/qt-4.8.4/bin/qmake -mpi -python > log.makePV3 2>&1
gzip < log.makePV3 > log.makePV3.gz

pwd
If all goes well, check the content of the file "log.makePV3" to see if it's any different.
If it still has the same problem, then I need the file "log.makePV3.gz", at least in case the message is different.

Best regards,
Bruno
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Old   November 28, 2015, 13:42
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Milan Šekularac
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First part, no error message and third command returs:
[username@localhost ThirdParty-2.3.0]$ ls -l platforms/linux64Gcc48/ParaView-4.1.0
ls: cannot access platforms/linux64Gcc48/ParaView-4.1.0: No such file or directory

* Should I run the second part and send you the log.makePV3.gz or no?


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Old   November 28, 2015, 13:47
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Sorry, I wrote incorrectly, I meant to write:
Quote:
If the third command tells you the path/file/folder doesn't exist, then run:
Quote:
Originally Posted by Milan2013 View Post

* Should I run the second part and send you the log.makePV3.gz or no?
Yes, please do run those commands.
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