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Segmentation Fault with ParaView After Upgrade |
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March 11, 2013, 22:11 |
Segmentation Fault with ParaView After Upgrade
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#1 |
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David Ouellette
Join Date: Feb 2013
Location: Ottawa, Ontario, Canada
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Hi all,
I recently upgraded OF to v2.2.0. However, whenever I run a case and view the results with paraView, I get the following error; whereby paraView just automatically closes. HTML Code:
Segmentation fault (core dumped) Code:
paraFoam -builtin Does anyone have any ideas on how to solve this problem? Thanks, David |
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March 25, 2013, 12:40 |
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#2 | ||
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I ran into the same problem and posted it on a new thread as I haven't seen this one. Here is what I posted:
------------------------------------ So, as suggested by another member here I was trying to run the motorBike example found in Quote:
Quote:
Code:
Running surfaceFeatureExtract on /home/OF_user/OpenFOAM/OF_user-2.2.0/run/tutorials/incompressible/simpleFoam/motorBike Running blockMesh on /home/OF_user/OpenFOAM/OF_user-2.2.0/run/tutorials/incompressible/simpleFoam/motorBike Running decomposePar on /home/OF_user/OpenFOAM/OF_user-2.2.0/run/tutorials/incompressible/simpleFoam/motorBike Running snappyHexMesh in parallel on /home/OF_user/OpenFOAM/OF_user-2.2.0/run/tutorials/incompressible/simpleFoam/motorBike using 6 processes Segmentation fault (core dumped) `0.org' -> `./processor0/0' `0.org/nut' -> `./processor0/0/nut' `0.org/include' -> `./processor0/0/include' `0.org/include/initialConditions' -> `./processor0/0/include/initialConditions' `0.org/include/frontBackUpperPatches' -> `./processor0/0/include/frontBackUpperPatches' `0.org/include/fixedInlet' -> `./processor0/0/include/fixedInlet' `0.org/omega' -> `./processor0/0/omega' `0.org/k' -> `./processor0/0/k' `0.org/p' -> `./processor0/0/p' `0.org/U' -> `./processor0/0/U' `0.org' -> `./processor1/0' `0.org/nut' -> `./processor1/0/nut' `0.org/include' -> `./processor1/0/include' `0.org/include/initialConditions' -> `./processor1/0/include/initialConditions' `0.org/include/frontBackUpperPatches' -> `./processor1/0/include/frontBackUpperPatches' `0.org/include/fixedInlet' -> `./processor1/0/include/fixedInlet' `0.org/omega' -> `./processor1/0/omega' `0.org/k' -> `./processor1/0/k' `0.org/p' -> `./processor1/0/p' `0.org/U' -> `./processor1/0/U' `0.org' -> `./processor2/0' `0.org/nut' -> `./processor2/0/nut' `0.org/include' -> `./processor2/0/include' `0.org/include/initialConditions' -> `./processor2/0/include/initialConditions' `0.org/include/frontBackUpperPatches' -> `./processor2/0/include/frontBackUpperPatches' `0.org/include/fixedInlet' -> `./processor2/0/include/fixedInlet' `0.org/omega' -> `./processor2/0/omega' `0.org/k' -> `./processor2/0/k' `0.org/p' -> `./processor2/0/p' `0.org/U' -> `./processor2/0/U' `0.org' -> `./processor3/0' `0.org/nut' -> `./processor3/0/nut' `0.org/include' -> `./processor3/0/include' `0.org/include/initialConditions' -> `./processor3/0/include/initialConditions' `0.org/include/frontBackUpperPatches' -> `./processor3/0/include/frontBackUpperPatches' `0.org/include/fixedInlet' -> `./processor3/0/include/fixedInlet' `0.org/omega' -> `./processor3/0/omega' `0.org/k' -> `./processor3/0/k' `0.org/p' -> `./processor3/0/p' `0.org/U' -> `./processor3/0/U' `0.org' -> `./processor4/0' `0.org/nut' -> `./processor4/0/nut' `0.org/include' -> `./processor4/0/include' `0.org/include/initialConditions' -> `./processor4/0/include/initialConditions' `0.org/include/frontBackUpperPatches' -> `./processor4/0/include/frontBackUpperPatches' `0.org/include/fixedInlet' -> `./processor4/0/include/fixedInlet' `0.org/omega' -> `./processor4/0/omega' `0.org/k' -> `./processor4/0/k' `0.org/p' -> `./processor4/0/p' `0.org/U' -> `./processor4/0/U' `0.org' -> `./processor5/0' `0.org/nut' -> `./processor5/0/nut' `0.org/include' -> `./processor5/0/include' `0.org/include/initialConditions' -> `./processor5/0/include/initialConditions' `0.org/include/frontBackUpperPatches' -> `./processor5/0/include/frontBackUpperPatches' `0.org/include/fixedInlet' -> `./processor5/0/include/fixedInlet' `0.org/omega' -> `./processor5/0/omega' `0.org/k' -> `./processor5/0/k' `0.org/p' -> `./processor5/0/p' `0.org/U' -> `./processor5/0/U' Running patchSummary in parallel on /home/OF_user/OpenFOAM/OF_user-2.2.0/run/tutorials/incompressible/simpleFoam/motorBike using 6 processes Segmentation fault (core dumped) Running potentialFoam in parallel on /home/OF_user/OpenFOAM/OF_user-2.2.0/run/tutorials/incompressible/simpleFoam/motorBike using 6 processes Segmentation fault (core dumped) Running simpleFoam in parallel on /home/OF_user/OpenFOAM/OF_user-2.2.0/run/tutorials/incompressible/simpleFoam/motorBike using 6 processes Segmentation fault (core dumped) Running reconstructParMesh on /home/OF_user/OpenFOAM/OF_user-2.2.0/run/tutorials/incompressible/simpleFoam/motorBike Running reconstructPar on /home/OF_user/OpenFOAM/OF_user-2.2.0/run/tutorials/incompressible/simpleFoam/motorBike Any idea what's the cause of this? Thanks. EDIT: Just wanted to say that the introductory "Cavity" tutorial worked just fine with the compiled OF, so my "newbie" guess is that it has to do with SnappyHexMesh. -------------------------------------------- Can anyone help? |
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March 25, 2013, 12:55 |
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#3 |
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David Ouellette
Join Date: Feb 2013
Location: Ottawa, Ontario, Canada
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Hey sudo,
What I found, in my case, was when I upgraded to OF 2.2.0, OF was still referring some of its files to my 2.1.1 installation, while others were referred to the 2.2.0 installation. Unfortunately, I'm not familiar enough with Linux to solve this problem, so the approach I took was reformatting my computer; which solved the problem. For me this approach wasn't a big deal since this computer is dedicated for running OF. And I realize that ideally you want to avoid this. So, hopefully someone else who is more familiar with Linux and OF would know how the solve this referencing problem (assuming this is the reason why your installation is not working). David |
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March 25, 2013, 14:21 |
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#4 |
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Thanks David,
In my case I compiled OF from source, it took like 3 hrs. to do that. I do not have this problem with the installed binary (same version) so I am thinking something went wrong with the compilation. I will give it a few days then recompile. |
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March 25, 2013, 16:46 |
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#5 |
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Bruno Santos
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Greetings to all!
What does your "~/.bashrc" file look like? Do the last few lines look something like the following : Code:
source /opt/openfoam211/etc/bashrc source /opt/openfoam220/etc/bashrc Code:
alias of211='source /opt/openfoam211/etc/bashrc' alias of220='source /opt/openfoam220/etc/bashrc' Then whenever you start a new terminal, decide which version you want, by running:
Code:
wmUNSET Best regards, Bruno
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March 26, 2013, 14:18 |
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#6 |
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Thanks Bruno but I don't think that's what I have wrong, see, since I compiled OF 2.2.0 from source, the last line of my .bashrc file (that I added per the installation instructions) is
Code:
source $HOME/OpenFOAM/OpenFOAM-2.2.0/etc/bashrc The one compiled from source is the one that is giving me the segmentation fault. |
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April 1, 2013, 09:14 |
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#7 |
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Bruno Santos
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Hi sudo,
OK, I've managed to take a look into this... could you attach the file "log.snappyHexMesh" that you should have in the "motorBike" folder. Because inside that file should be the whole story as to why it crashed! Best regards, Bruno
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April 1, 2013, 12:50 |
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#8 |
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Easy as pie, here:
File: log.snappyHexMesh Code:
-------------------------------------------------------------------------- Sorry! You were supposed to get help about: find-available:not-valid But I couldn't open the help file: /home/OF_user/OpenFOAM/ThirdParty-2.2.0/platforms/linux64Gcc/openmpi-1.6.3/share/openmpi/help-mca-base.txt: No such file or directory. Sorry! -------------------------------------------------------------------------- [ZeusUbuntu:30295] *** Process received signal *** [ZeusUbuntu:30295] Signal: Segmentation fault (11) [ZeusUbuntu:30295] Signal code: Address not mapped (1) [ZeusUbuntu:30295] Failing at address: 0x28 [ZeusUbuntu:30295] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xfcb0) [0x7fc8dda9dcb0] [ZeusUbuntu:30295] [ 1] /usr/lib/libopen-pal.so.0(mca_base_select+0x106) [0x7fc8ddccd7b6] [ZeusUbuntu:30295] [ 2] /usr/lib/libopen-pal.so.0(opal_crs_base_select+0x7e) [0x7fc8ddcdfdae] [ZeusUbuntu:30295] [ 3] /usr/lib/libopen-pal.so.0(opal_cr_init+0x303) [0x7fc8ddcbe3a3] [ZeusUbuntu:30295] [ 4] /usr/lib/libopen-pal.so.0(opal_init+0x17b) [0x7fc8ddcbdd0b] [ZeusUbuntu:30295] [ 5] /usr/lib/libopen-rte.so.0(orte_init+0x4f) [0x7fc8ddf10aff] [ZeusUbuntu:30295] [ 6] mpirun() [0x40311f] [ZeusUbuntu:30295] [ 7] mpirun() [0x402c9c] [ZeusUbuntu:30295] [ 8] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) [0x7fc8dd6f076d] [ZeusUbuntu:30295] [ 9] mpirun() [0x402b99] [ZeusUbuntu:30295] *** End of error message ** |
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April 1, 2013, 13:27 |
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#9 | |
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Bruno Santos
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Hi sudo,
Wicked error... but it seems familiar. OK, let's try and isolate-and-conquer this thing... 1. Right after you've executed Allrun, try this: Code:
foamJob -s -p snappyHexMesh -overwrite 2. If it does, check the first couple of lines after you've executed that command... you should find something like this: Code:
Executing: /usr/bin/mpirun -np 6 /opt/openfoam220/bin/foamExec -prefix /opt snappyHexMesh -overwrite -parallel | tee log 3. The error given is likely to either be related to something in the path above, such as a reference to a "machines" file, or it is because there is some network card/interface in the way... I have a reference to a solution on my blog post "Notes about running OpenFOAM in parallel", namely "decomposed case to 2-cores (Not working) (more precisely post #21 has valuable info)"... and I quote: Quote:
Bruno
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April 1, 2013, 13:45 |
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#10 |
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So I did:
Code:
$ ./Allrun Code:
$ foamJob -s -p snappyHexMesh -overwrite Code:
Parallel processing using OPENMPI with 6 processors Executing: /usr/bin/mpirun -np 6 /home/OF_user/OpenFOAM/OpenFOAM-2.2.0/bin/foamExec -prefix /home/OF_user/OpenFOAM snappyHexMesh -overwrite -parallel | tee log -------------------------------------------------------------------------- Sorry! You were supposed to get help about: find-available:not-valid But I couldn't open the help file: /home/OF_user/OpenFOAM/ThirdParty-2.2.0/platforms/linux64Gcc/openmpi-1.6.3/share/openmpi/help-mca-base.txt: No such file or directory. Sorry! -------------------------------------------------------------------------- [ZeusUbuntu:31971] *** Process received signal *** [ZeusUbuntu:31971] Signal: Segmentation fault (11) [ZeusUbuntu:31971] Signal code: Address not mapped (1) [ZeusUbuntu:31971] Failing at address: 0x28 [ZeusUbuntu:31971] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xfcb0) [0x7f8cd2376cb0] [ZeusUbuntu:31971] [ 1] /usr/lib/libopen-pal.so.0(mca_base_select+0x106) [0x7f8cd25a67b6] [ZeusUbuntu:31971] [ 2] /usr/lib/libopen-pal.so.0(opal_crs_base_select+0x7e) [0x7f8cd25b8dae] [ZeusUbuntu:31971] [ 3] /usr/lib/libopen-pal.so.0(opal_cr_init+0x303) [0x7f8cd25973a3] [ZeusUbuntu:31971] [ 4] /usr/lib/libopen-pal.so.0(opal_init+0x17b) [0x7f8cd2596d0b] [ZeusUbuntu:31971] [ 5] /usr/lib/libopen-rte.so.0(orte_init+0x4f) [0x7f8cd27e9aff] [ZeusUbuntu:31971] [ 6] /usr/bin/mpirun() [0x40311f] [ZeusUbuntu:31971] [ 7] /usr/bin/mpirun() [0x402c9c] [ZeusUbuntu:31971] [ 8] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) [0x7f8cd1fc976d] [ZeusUbuntu:31971] [ 9] /usr/bin/mpirun() [0x402b99] [ZeusUbuntu:31971] *** End of error message *** Segmentation fault (core dumped) Last edited by sudo; April 1, 2013 at 14:47. |
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April 1, 2013, 13:48 |
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#11 |
Retired Super Moderator
Bruno Santos
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The last quote in my previous post already has the possible solution, which is to specify which network interfaces to ignore. Said interfaces have to be listed directly using the mpirun line.
To know which network interfaces your system has got, you can run: Code:
ifconfig -a
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April 1, 2013, 15:10 |
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#12 |
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Ok, so:
1. I ran Code:
$ ifconfig -a Code:
eth0 Link encap:Ethernet HWaddr 00:24:8c:a7:21:f2 UP BROADCAST MULTICAST MTU:1500 Metric:1 RX packets:0 errors:0 dropped:0 overruns:0 frame:0 TX packets:0 errors:0 dropped:0 overruns:0 carrier:0 collisions:0 txqueuelen:1000 RX bytes:0 (0.0 B) TX bytes:0 (0.0 B) Interrupt:16 Memory:fbee0000-fbf00000 eth1 Link encap:Ethernet HWaddr 00:24:8c:a7:22:5d inet addr:192.168.98.106 Bcast:192.168.98.255 Mask:255.255.255.0 inet6 addr: fe80::224:8cff:fea7:225d/64 Scope:Link UP BROADCAST RUNNING MULTICAST MTU:1500 Metric:1 RX packets:357135 errors:0 dropped:0 overruns:0 frame:0 TX packets:136298 errors:0 dropped:0 overruns:0 carrier:0 collisions:0 txqueuelen:1000 RX bytes:358853304 (358.8 MB) TX bytes:15173962 (15.1 MB) Interrupt:17 Memory:fbde0000-fbe00000 lo Link encap:Local Loopback inet addr:127.0.0.1 Mask:255.0.0.0 inet6 addr: ::1/128 Scope:Host UP LOOPBACK RUNNING MTU:16436 Metric:1 RX packets:6858 errors:0 dropped:0 overruns:0 frame:0 TX packets:6858 errors:0 dropped:0 overruns:0 carrier:0 collisions:0 txqueuelen:0 RX bytes:658163 (658.1 KB) TX bytes:658163 (658.1 KB) Code:
$ mpirun --mca btl_tcp_if_exclude lo,eth0,eth1 Code:
-------------------------------------------------------------------------- Sorry! You were supposed to get help about: orterun:executable-not-specified But I couldn't open the help file: /home/OF_user/OpenFOAM/ThirdParty-2.2.0/platforms/linux64Gcc/openmpi-1.6.3/share/openmpi/help-orterun.txt: No such file or directory. Sorry! -------------------------------------------------------------------------- 3. I even tried to exclude TCP all together Code:
$ mpirun --mca btl ^tcp Code:
-------------------------------------------------------------------------- OF_user@ZeusUbuntu:motorBike$ mpirun --mca btl ^tcp -------------------------------------------------------------------------- Sorry! You were supposed to get help about: orterun:executable-not-specified But I couldn't open the help file: /home/OF_user/OpenFOAM/ThirdParty-2.2.0/platforms/linux64Gcc/openmpi-1.6.3/share/openmpi/help-orterun.txt: No such file or directory. Sorry! -------------------------------------------------------------------------- |
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April 1, 2013, 15:22 |
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#13 |
Retired Super Moderator
Bruno Santos
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You forgot the rest of the train namely:
Code:
-np 6 /home/OF_user/OpenFOAM/OpenFOAM-2.2.0/bin/foamExec -prefix /home/OF_user/OpenFOAM snappyHexMesh -overwrite -parallel | tee log Code:
mpirun --mca btl_tcp_if_exclude lo,eth0,eth1 -np 6 /home/OF_user/OpenFOAM/OpenFOAM-2.2.0/bin/foamExec -prefix /home/OF_user/OpenFOAM snappyHexMesh -overwrite -parallel | tee log Code:
mpirun --mca btl ^tcp -np 6 /home/OF_user/OpenFOAM/OpenFOAM-2.2.0/bin/foamExec -prefix /home/OF_user/OpenFOAM snappyHexMesh -overwrite -parallel | tee log
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April 1, 2013, 15:57 |
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#14 |
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Ok, fair enough but it didn't make any difference, and I think I know why .
From the annoying error message about the missing file, it seems that OF is set up to use the Openmpi 1.6.3 that shipped with vesion 2.2.0, thing is I never compiled it! The Openmpi I have is version 1.4.5 that I installed from Ubuntu 12.10 repos to compile OF. So, in short, do I just follow the instructions in the "INSTALL" file and compile Openmpi 1.6.3 via $ configure and $ make all install? So no wmake? And do I have to uninstall the old version? Just wanna be sure. Thanks a lot Bruno, your help is much appreciated. |
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April 1, 2013, 18:37 |
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#15 |
Retired Super Moderator
Bruno Santos
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Hi sudo,
OK, edit the file "$WM_PROJECT_DIR/etc/bashrc"... you can see it's path by running: Code:
echo "$WM_PROJECT_DIR/etc/bashrc" Code:
export WM_MPLIB=OPENMPI Code:
export WM_MPLIB=SYSTEMOPENMPI If it still has problems, go to OpenFOAM's folder and run Allwmake once again: Code:
cd $WM_PROJECT_DIR ./Allwmake > make.log 2>&1 Then try once again running in parallel... hopefully it will now work, ot at least give a proper error message Best regards, Bruno
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April 1, 2013, 18:59 |
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#16 |
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AWESOME!!! There is at least something to celebrate, the previous error (segmentation fault) is gone. In more details:
1. I did these, just as Bruno suggested. Code:
echo "$WM_PROJECT_DIR/etc/bashrc" Code:
export WM_MPLIB=OPENMPI Code:
export WM_MPLIB=SYSTEMOPENMPI Code:
--> FOAM FATAL ERROR: Trying to use the dummy Pstream library. This dummy library cannot be used in parallel mode From function UPstream::init(int& argc, char**& argv) in file UPstream.C at line 37. FOAM exiting Last edited by sudo; April 1, 2013 at 19:16. |
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April 2, 2013, 18:24 |
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#17 |
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I finally did this:
Code:
cd $WM_PROJECT_DIR ./Allwmake > make.log 2>&1 |
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