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

[foam-extend.org] foam-extend-4.0 install not as root

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

Like Tree1Likes
  • 1 Post By treem22

Reply
 
LinkBack Thread Tools Search this Thread Display Modes
Old   February 27, 2019, 16:38
Default foam-extend-4.0 install not as root
  #1
Member
 
Mike Tree
Join Date: Feb 2016
Location: Charlotte, NC
Posts: 36
Rep Power: 9
treem22 is on a distinguished road
I am attempting to install foam-extend-4.0 on a file system in which I am not root. Of course, I'm in a bit over my head and this isn't working out.

When running the following command:

Code:
./Allwmake | tee make.log
I'm met with the following:

Code:
   1 make: Nothing to be done for `all'.
   2 + wmakePrintBuild -check
   3  same version as previous build
   4 + wmakeLnInclude foam
   5 + wmakeLnInclude meshTools
   6 + wmakeLnInclude OSspecific/POSIX
   7 + wmake libo OSspecific/POSIX
   8 '/beegfs/users/mtree/foam/foam-extend-4.0/lib/linux64GccDPOpt/libOSspecific.o' is up to date.
   9 + set +x
  10
  11 Note: ignore spurious warnings about missing mpicxx.h headers
  12 + wmake libso foam
  13 SOURCE=global/global.Cver ; sed -e 's/VERSION_STRING/4.0/' -e 's/BUILD_STRING/4.0-268bb07d15d8/' $SOURCE > Make/linux64GccDPOpt/global.C; g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-u
  14 /usr/bin/ld: cannot find -lmpi
  15 /usr/bin/ld: skipping incompatible /lib/libm.so when searching for -lm
  16 /usr/bin/ld: skipping incompatible /lib/libc.so when searching for -lc
  17 collect2: error: ld returned 1 exit status
  18 make: *** [/beegfs/users/mtree/foam/foam-extend-4.0/lib/linux64GccDPOpt/libfoam.so] Error 1
  19 + decompositionMethods/AllwmakeLnInclude
  20 + wmakeLnInclude decompositionMethods
  21 + wmakeLnInclude metisDecomp
  22 + wmakeLnInclude parMetisDecomp
  23 + wmakeLnInclude scotchDecomp
  24 + decompositionMethods/Allwmake
  25 + wmakeLnInclude decompositionMethods
  26 + wmake libso decompositionMethods
  27 '/beegfs/users/mtree/foam/foam-extend-4.0/lib/linux64GccDPOpt/libdecompositionMethods.so' is up to date
  28 + wmake libso metisDecomp
  29 SOURCE=metisDecomp.C ;  g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3  -DNoRepository -ftemplate-depth-200 -I     -I../decomposi
  30 In file included from metisDecomp.C:26:0:
  31 metisDecomp.H:38:33: fatal error: decompositionMethod.H: No such file or directory
  32 compilation terminated.
  33 make: *** [Make/linux64GccDPOpt/metisDecomp.o] Error 1
  34 + wmake libso parMetisDecomp
  35 SOURCE=parMetisDecomp.C ;  g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3  -DNoRepository -ftemplate-depth-200 -DOMPI_SKIP_MPICXX
  36 In file included from parMetisDecomp.C:26:0:
  37 parMetisDecomp.H:37:33: fatal error: decompositionMethod.H: No such file or directory
  38 compilation terminated.
  39 make: *** [Make/linux64GccDPOpt/parMetisDecomp.o] Error 1
  40 + wmake libso scotchDecomp
  41 SOURCE=scotchDecomp/scotchDecomp.C ;  g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3  -DNoRepository -ftemplate-depth-200 -I     
  42 SOURCE=engineScotchDecomp/engineScotchDecomp.C ;  g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3  -DNoRepository -ftemplate-depth
  43 In file included from scotchDecomp/scotchDecomp.C:107:0:
  44 scotchDecomp/scotchDecomp.H:38:33: fatal error: decompositionMethod.H: No such file or directory
  45 compilation terminated.
  46 In file included from engineScotchDecomp/engineScotchDecomp.H:49:0,  
  47                  from engineScotchDecomp/engineScotchDecomp.C:
  48 lnInclude/scotchDecomp.H:38:33: fatal error: decompositionMethod.H: No such file or directory
  49 compilation terminated.
  50 make: *** [Make/linux64GccDPOpt/engineScotchDecomp.o] Error 1
  51 make: *** Waiting for unfinished jobs....
  52 make: *** [Make/linux64GccDPOpt/scotchDecomp.o] Error 1
  53 + wmake libso lagrangian/basic
  54 '/beegfs/users/mtree/foam/foam-extend-4.0/lib/linux64GccDPOpt/liblagrangian.so' is up to date.
  55 + wmake libso edgeMesh
  56 '/beegfs/users/mtree/foam/foam-extend-4.0/lib/linux64GccDPOpt/libedgeMesh.so' is up to date.
  57 + wmake libso surfMesh
  58 '/beegfs/users/mtree/foam/foam-extend-4.0/lib/linux64GccDPOpt/libsurfMesh.so' is up to date.
  59 + wmake libso meshTools
  60 '/beegfs/users/mtree/foam/foam-extend-4.0/lib/linux64GccDPOpt/libmeshTools.so' is up to date.
  61 + wmake libso finiteVolume
  62 '/beegfs/users/mtree/foam/foam-extend-4.0/lib/linux64GccDPOpt/libfiniteVolume.so' is up to date.
  63 + wmake libso finiteArea
  64 '/beegfs/users/mtree/foam/foam-extend-4.0/lib/linux64GccDPOpt/libfiniteArea.so' is up to date.
  65 + wmake libso lduSolvers
  66 '/beegfs/users/mtree/foam/foam-extend-4.0/lib/linux64GccDPOpt/liblduSolvers.so' is up to date.
  67 + wmake libso tetFiniteElement
  68 '/beegfs/users/mtree/foam/foam-extend-4.0/lib/linux64GccDPOpt/libtetFiniteElement.so' is up to date.
  69 + dynamicMesh/AllwmakeLnInclude
  70 + wmakeLnInclude dynamicMesh
  71 + wmakeLnInclude dynamicFvMesh
  72 + wmakeLnInclude topoChangerFvMeshG
The following files are also attached, and may be helpful:
  • etc/settings.sh
  • etc/bashrc

I have no prefs.sh file.

Running foamInstallationTest provides the following:

Code:
  4 Checking basic setup...                                                                                                                                                                   
  5 -------------------------------------------------------------------------------
  6 Shell:              bash                                                                                                                                                                  
  7 Host:               corvidpost7.corvidtec.com                                                                                                                                             
  8 OS:                 Linux version 3.10.0-957.1.3.el7.x86_64                                                                                                                               
  9 -------------------------------------------------------------------------------                                                                                                           
 10                                                                                                                                                                                           
 11                                                                                                                                                                                           
 12 Checking main foam-extend env variables...                                                                                                                                                
 13 -------------------------------------------------------------------------------                                                                                                           
 14 Environment_variable Set_to_file_or_directory                Valid      Crit                                                                                                              
 15 -------------------------------------------------------------------------------                                                                                                           
 16 $WM_PROJECT_INST_DIR /beegfs/users/mtree/foam                 yes       yes                                                                                                               
 17 $WM_PROJECT_USER_DIR /beegfs/users/mtree/foam/mtree-4.0       no        no                                                                                                                
 18 $WM_THIRD_PARTY_DIR  ...tree/foam/foam-extend-4.0/ThirdParty  yes       yes                                                                                                               
 19 -------------------------------------------------------------------------------                                                                                                           
 20                                                                                                                                                                                           
 21                                                                                                                                                                                           
 22 Checking the foam-extend env variables set on the PATH...                                                                                                                                 
 23 -------------------------------------------------------------------------------                                                                                                           
 24 Environment_variable Set_to_file_or_directory                Valid Path Crit                                                                                                              
 25 -------------------------------------------------------------------------------                                                                                                           
 26 $WM_PROJECT_DIR      /beegfs/users/mtree/foam/foam-extend-4.0  yes  yes  yes                                                                                                              
 27                                                                                                                                                                                           
 28 $FOAM_APPBIN         ...4.0/applications/bin/linux64GccDPOpt  yes  yes  yes                                                                                                               
 29 $FOAM_SITE_APPBIN    ...ee/foam/site/4.0/bin/linux64GccDPOpt  yes  yes  no                                                                                                                
 30 $FOAM_USER_APPBIN    ...4.0/applications/bin/linux64GccDPOpt  no        no                                                                                                                
 31 $WM_DIR              ...ers/mtree/foam/foam-extend-4.0/wmake  yes  yes  yes                                                                                                               
 32 -------------------------------------------------------------------------------                                                                                                           
 33                                                                                                                                                                                           
 34                                                                                                                                                                                           
 35 Checking the foam-extend env variables set on the LD_LIBRARY_PATH...                                                                                                                      
 36 -------------------------------------------------------------------------------                                                                                                           
 37 Environment_variable Set_to_file_or_directory                Valid Path Crit                                                                                                              
 38 -------------------------------------------------------------------------------                                                                                                           
 39 $FOAM_LIBBIN         .../foam-extend-4.0/lib/linux64GccDPOpt  yes  yes  yes                                                                                                               
 40 $FOAM_SITE_LIBBIN    ...ee/foam/site/4.0/lib/linux64GccDPOpt  yes  yes  no                                                                                                                
 41 $FOAM_USER_LIBBIN    ...e/foam/mtree-4.0/lib/linux64GccDPOpt  no        no                                                                                                                
 42 $MPI_ARCH_PATH       --------- env variable not set ---------            yes                                                                                                              
 43 -------------------------------------------------------------------------------
 44                                                                                                                                                                                           
 45                                                                                                                                                                                           
 46 Third party software                                                                                                                                                                      
 47 -------------------------------------------------------------------------------                                                                                                           
 48 Software Version   Location                                                                                                                                                               
 49 -------------------------------------------------------------------------------                                                                                                           
 50 WARNING: gcc version does not match gcc supplied with this release of foam-extend                                                                                                         
 51          Supplied version: 4.3.3                                                                                                                                                          
 52          User version    : 5.4.0                                                                                                                                                          
 53          Minimum required: 4.3.1                                                                                                                                                          
 54                                                                                                                                                                                           
 55 gcc      5.4.0                                                                                                                                                                            
 56 WARNING:  Conflicting installations:                                                                                                                                                      
 57           foam-extend settings        : /bin/gcc                                                                                                                                          
 58           current path             : /opt/Software/gcc/5.4.0/bin/gcc                                                                                                                      
 59           CRITICAL ERROR                                                                                                                                                                  
 60                                                                                                                                                                                           
 61 gzip     1.5       /usr/bin/gzip                                                                                                                                                          
 62 tar      1.26      /usr/bin/tar                                                                                                                                                           
 63 icoFoam                                                                                                                                                                                   
 64 WARNING:  Conflicting installations:                                                                                                                                                      
 65           foam-extend settings        : /beegfs/users/mtree/foam/foam-extend-4.0/applications/bin/linux64GccDPOpt/icoFoam                                                                 
 66           current path             :                                                                                                                                                      
 67           CRITICAL ERROR                                                                                                                                                                  
 68                                                                                                                                                                                           
 69 -------------------------------------------------------------------------------                                                                                                           
 70                                                                                                                                                                                           
 71                                                                                                                                                                                           
 72 Summary                                                                                                                                                                                   
 73 -------------------------------------------------------------------------------                                                                                                           
 74 Base configuration ok.                                                                                                                                                                    
 75                                                                                                                                                                                           
 76 The foam installation contains 2 critical error(s).                                                                                                                                       
 77                                                                                                                                                                                           
 78 Review the output for warning messages and consult                                                                                                                                        
 79 the installation guide for trouble shooting.                                                                                                                                              
 80                                                                                                                                                                                           
 81 done.
Attached Files
File Type: txt settings.sh.txt (28.2 KB, 6 views)
File Type: txt bashrc.txt (16.4 KB, 7 views)
treem22 is offline   Reply With Quote

Old   February 27, 2019, 18:57
Default
  #2
Retired Super Moderator
 
Bruno Santos
Join Date: Mar 2009
Location: Lisbon, Portugal
Posts: 10,969
Blog Entries: 45
Rep Power: 127
wyldckat is a name known to allwyldckat is a name known to allwyldckat is a name known to allwyldckat is a name known to allwyldckat is a name known to allwyldckat is a name known to all
Quick questions:
  1. Which Linux Distribution are you using?
    • From the output you've provided, I'm guessing it's CentOS 7?
  2. Which installation instructions are you following?
  3. If you did follow the instructions from the wiki page, then did you do anything different from the instructions given there?
  4. The output you've provided is too incomplete. Please run the following commands:
    Code:
    ./Allwmake > log.make 2>&1
    gzip < log.make > log.make.gz
    Then attach the file "log.make.gz" to your next post.
__________________
wyldckat is offline   Reply With Quote

Old   February 28, 2019, 15:05
Default
  #3
Member
 
Mike Tree
Join Date: Feb 2016
Location: Charlotte, NC
Posts: 36
Rep Power: 9
treem22 is on a distinguished road
wyldckat,

I am running on Scientific Linux release 7.6 (Nitrogen)

I started out following the instructions on the wiki, but then got side-tracked trying different things to get the install to complete. I don't remember all the steps, so I started over.

With a clean slate, I then performed the following steps to arrive at the log.make.gz file that is attached:
  1. cloned git repo as instructed on wiki
  2. ran ./Allwmake.firstInstall as instructed on wiki (without installing Paraview b/c it's already installed)
  3. ran ./maintainanceScripts/UpdateSpecialDependencies.sh from /swak4Foam-0.4.0/ directory as suggested by output from previous step
  4. added ThirdParty/rpmbuild/BUILD/swak4Foam-0.4.0/privateRequirements/bin to $PATH as suggested by output from step 3
  5. ran ./Allwmake > log.make 2>&1; gzip < log.make > log.make.gz from /foam-extend-4.0/ directory

foamInstallationTest still complains that $MPI_ARCH_PATH is not set and that gcc has conflicting installations

Thanks for your help!

MT
Attached Files
File Type: gz log.make.gz (4.8 KB, 4 views)
treem22 is offline   Reply With Quote

Old   February 28, 2019, 17:17
Default
  #4
Retired Super Moderator
 
Bruno Santos
Join Date: Mar 2009
Location: Lisbon, Portugal
Posts: 10,969
Blog Entries: 45
Rep Power: 127
wyldckat is a name known to allwyldckat is a name known to allwyldckat is a name known to allwyldckat is a name known to allwyldckat is a name known to allwyldckat is a name known to all
Quick answers:
  1. The "log.make" file states that everything is just fine.
  2. Please try using foam-extend, for example, by running:
    Code:
    blockMesh -help
    If it gives some help information and does not complain something about MPI, then it should work just fine as well.
  3. foamInstallationTest is likely outdated and does not properly check for requirements, therefore you might as well ignore it.
wyldckat is offline   Reply With Quote

Old   March 1, 2019, 07:56
Default
  #5
Member
 
Mike Tree
Join Date: Feb 2016
Location: Charlotte, NC
Posts: 36
Rep Power: 9
treem22 is on a distinguished road
Yep, blockMesh seems to be working. No complaints about MPI. Guess I was worried about nothing.

Thanks!
wyldckat likes this.
treem22 is offline   Reply With Quote

Old   February 25, 2020, 11:49
Default
  #6
Member
 
Thomas
Join Date: Nov 2017
Posts: 37
Rep Power: 7
hand90 is on a distinguished road
Hi everyone

I am aware that this post is a few years old and there was never really an issue in the first place. However my issue is that I cannot install foam extend 4.0 on Centos 7. As I believe that the problem is the missing rpm-build package and I cannot install it due to no root access, I thought I post my problem here.

The issue is that none of the ThirdParty packages are installed. They download properly but the folder RPMS stays empty.

I can see that:
"tools/makeThirdPartyFunctionsForRPM: line 180: rpmbuild: command not found"

when checking if rpmbuild is available,
"rpm rpm-build q"
it is not and as I don't have root access I cannot build it.

Does anyone have any suggestions on how I can install foam-extend 4.0 on CentOS 7?
hand90 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
[CGNS] CGNS converters available mbeaudoin OpenFOAM Meshing & Mesh Conversion 137 December 14, 2018 04:20
[mesh manipulation] Importing Multiple Meshes thomasnwalshiii OpenFOAM Meshing & Mesh Conversion 18 December 19, 2015 18:57
decomposePar is missing a library whk1992 OpenFOAM Pre-Processing 8 March 7, 2015 07:53
missing vtf3.h BPatch.h papi.h linch OpenFOAM Installation 41 July 24, 2012 14:45
[blockMesh] error message with modeling a cube with a hold at the center hsingtzu OpenFOAM Meshing & Mesh Conversion 2 March 14, 2012 09:56


All times are GMT -4. The time now is 21:08.