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[foam-extend.org] foam-extend-4.0 Debian Testing bison problem fseterr.c |
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May 21, 2019, 18:29
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foam-extend-4.0 Debian Testing bison problem fseterr.c
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#1 |
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New Member
bret
Join Date: May 2019
Posts: 7
Rep Power: 7  |
Hello, I recently attained this computer from our work group at school. It 'had' some version of foam-extend on it but no longer. It does have OPENMPI, PARAVIEW and other 'programming' things on it. It is DEBIAN TESTING and current. Also, the prerequisites;
Code:
sbh@sbh:~/foam/foam-extend-4.0$ sudo apt-cache policy git build-essential binutils-dev cmake flex zlib1g-dev qt4-dev-tools libqt4-dev libncurses5-dev libxt-dev rpm mercurial graphviz python python-dev libiberty-dev | grep -e "Installed" -B 1 git: Installed: 1:2.20.1-2 -- build-essential: Installed: 12.6 -- binutils-dev: Installed: 2.31.1-16 -- cmake: Installed: 3.13.4-1 -- flex: Installed: 2.6.4-6.2 -- zlib1g-dev: Installed: 1:1.2.11.dfsg-1 -- qt4-dev-tools: Installed: 4:4.8.7+dfsg-18 -- libqt4-dev: Installed: 4:4.8.7+dfsg-18 -- libncurses5-dev: Installed: 6.1+20181013-2 -- libxt-dev: Installed: 1:1.1.5-1+b3 -- rpm: Installed: 4.14.2.1+dfsg1-1 -- mercurial: Installed: 4.8.2-1 -- graphviz: Installed: 2.40.1-6 -- python: Installed: 2.7.16-1 -- python-dev: Installed: 2.7.16-1 -- libiberty-dev: Installed: 20190122-1 Code:
sbh@sbh:~/foam/foam-extend-4.0$ gcc --version gcc (Debian 8.3.0-6) 8.3.0 Code:
sbh@sbh:~/foam/foam-extend-4.0$ ./bin/foamInstallationTest
Executing ./bin/foamInstallationTest:
Checking basic setup...
-------------------------------------------------------------------------------
Shell: bash
Host: sbh
OS: Linux version 4.19.0-5-amd64
-------------------------------------------------------------------------------
Checking main foam-extend env variables...
-------------------------------------------------------------------------------
Environment_variable Set_to_file_or_directory Valid Crit
-------------------------------------------------------------------------------
$WM_PROJECT_INST_DIR /home/sbh/foam yes yes
$WM_PROJECT_USER_DIR /home/sbh/foam/sbh-4.0 no no
$WM_THIRD_PARTY_DIR .../sbh/foam/foam-extend-4.0/ThirdParty yes yes
-------------------------------------------------------------------------------
Checking the foam-extend env variables set on the PATH...
-------------------------------------------------------------------------------
Environment_variable Set_to_file_or_directory Valid Path Crit
-------------------------------------------------------------------------------
$WM_PROJECT_DIR /home/sbh/foam/foam-extend-4.0 yes yes yes
$FOAM_APPBIN ...4.0/applications/bin/linux64GccDPOpt yes yes yes
$FOAM_SITE_APPBIN ...bh/foam/site/4.0/bin/linux64GccDPOpt no no
$FOAM_USER_APPBIN ...4.0/applications/bin/linux64GccDPOpt no no
$WM_DIR /home/sbh/foam/foam-extend-4.0/wmake yes yes yes
-------------------------------------------------------------------------------
Checking the foam-extend env variables set on the LD_LIBRARY_PATH...
-------------------------------------------------------------------------------
Environment_variable Set_to_file_or_directory Valid Path Crit
-------------------------------------------------------------------------------
$FOAM_LIBBIN .../foam-extend-4.0/lib/linux64GccDPOpt yes yes yes
$FOAM_SITE_LIBBIN ...bh/foam/site/4.0/lib/linux64GccDPOpt no no
$FOAM_USER_LIBBIN ...sbh/foam/sbh-4.0/lib/linux64GccDPOpt no no
$MPI_ARCH_PATH /usr yes yes yes
-------------------------------------------------------------------------------
Third party software
-------------------------------------------------------------------------------
Software Version Location
-------------------------------------------------------------------------------
WARNING: gcc version does not match gcc supplied with this release of foam-extend
Supplied version: 4.3.3
User version : 8.3.0
Minimum required: 4.3.1
gcc 8.3.0
WARNING: Conflicting installations:
foam-extend settings : /bin/gcc
current path : /usr/bin/gcc
CRITICAL ERROR
gzip 1.9 /usr/bin/gzip
tar 1.30 /usr/bin/tar
icoFoam
WARNING: Conflicting installations:
foam-extend settings : /home/sbh/foam/foam-extend-4.0/applications/bin/linux64GccDPOpt/icoFoam
current path :
CRITICAL ERROR
-------------------------------------------------------------------------------
Summary
-------------------------------------------------------------------------------
Base configuration ok.
The foam installation contains 2 critical error(s).
Review the output for warning messages and consult
the installation guide for trouble shooting.
done.
openmpi-bin has binaries in /usr/bin/ and openmpi-common has txt files in /usr/share/ and libopenmpi-dev (all 3.1.3-11) has libraries in /usr/lib/x86_64-linux-gnu/openmpi/... Speaking of libraries, I did read that openmpi has some weird issue with $LD_LIBRARY_PATH (can't find the website at the moment), so here is that PATH; Code:
/home/sbh/foam/sbh-4.0/lib/linux64GccDPOpt:/home/sbh/foam/site/4.0/lib/linux64GccDPOpt:/home/sbh/foam/foam-extend-4.0/lib/linux64GccDPOpt:/home/sbh/SW/Cantera/installed/lib:/usr/lib:/usr/lib/x86_64-linux-gnu /bin is a symbolic link to /usr/bin, verified by ls -ld /bin. Then, from here, https://openfoamwiki.net/index.php/I...end-4.0/Ubuntu I've tried all the prerequisite requirements except for gcc-5 (it's not in my repositories though I suppose I could find them somewhere if it is heavily suggested - partly why I am posting this question. Pinning various repositories is not something I'm too interested in... FrankenDebian). From here, https://openfoamwiki.net/index.php/I...oam-extend-4.0, I have tried the installation (I don't specifically have Ubuntu or OpenSUSE so I think I mostly try to go with Ubuntu). I've also tried the instructions (for my initial attempt of foam-extend-4.1) from this site, https://pingpong.chalmers.se/public/...ml?language=en but it didn't work for me. In a fresh git pull, my etc/bashrc was left alone and my etc/prefs.sh utilized, Code:
export QT_BIN_DIR=/usr/bin/ export WM_THIRD_PARTY_USE_BISON_27=1 #export MPI_ARCH_PATH=/usr/bin/ export WM_MPLIB=SYSTEMOPENMPI export OPENMPI_DIR=/usr export OPENMPI_BIN_DIR=\$OPENMPI_DIR/bin I found the installationTest later but earlier I did try going into the ThirdParty/rpmBuild/SOURCES/ and trying to untar different bisons I got from https://ftp.gnu.org/gnu/bison/ and then changing their name to match 2.7.1. They all (even the 2.6.5 and others) complained of this fseterr.c problem. Well I'll stop now as I think I need help to go further. Thank you for reading this far! Bret PS. I'll gladly start over and follow someone's kind instructions! I also did this for the logs (running Allwmake.firstInstall twice [big one first and split into parts, smaller file second as log2.gz]), as noted in https://pingpong.chalmers.se/public/...ml?language=en and the first error I found is; Code:
make[3]: Entering directory '/home/sbh/foam/foam-extend-4.0/ThirdParty/rpmBuild/BUILD/bison-2.7/lib'
CC main.o
CC yyerror.o
CC argmatch.o
CC binary-io.o
CC bitrotate.o
CC c-ctype.o
CC c-strncasecmp.o
CC c-strcasecmp.o
CC cloexec.o
CC close-stream.o
CC closeout.o
CC dirname.o
CC basename.o
CC dirname-lgpl.o
CC basename-lgpl.o
CC stripslash.o
CC exitfail.o
CC fatal-signal.o
CC fd-hook.o
CC fd-safer-flag.o
CC dup-safer-flag.o
CC fopen-safer.o
CC hash.o
CC localcharset.o
CC lock.o
CC math.o
CC mbchar.o
CC mbschr.o
CC mbsrchr.o
CC mbswidth.o
CC mbuiter.o
CC pipe2.o
CC pipe2-safer.o
CC printf-frexp.o
CC printf-frexpl.o
CC progname.o
CC quotearg.o
CC sig-handler.o
CC spawn-pipe.o
CC stdio.o
CC strnlen1.o
CC threadlib.o
CC unistd.o
CC dup-safer.o
CC fd-safer.o
CC pipe-safer.o
CC width.o
CC wait-process.o
CC wctype-h.o
CC xmalloc.o
CC xalloc-die.o
CC xsize.o
CC xstrndup.o
CC get-errno.o
CC abitset.o
CC bitset.o
CC bitset_stats.o
CC bitsetv.o
CC ebitset.o
CC vbitset.o
CC lbitset.o
CC bitsetv-print.o
CC timevar.o
CC asnprintf.o
CC fcntl.o
CC fprintf.o
CC fseterr.o
CC isnand.o
CC isnanf.o
CC isnanl.o
CC printf.o
fseterr.c: In function 'fseterr':
fseterr.c:77:3: error: #error "Please port gnulib fseterr.c to your platform! Look at the definitions of ferror and clearerr on your system, then report this to bug-gnulib."
#error "Please port gnulib fseterr.c to your platform! Look at the definitions of ferror and clearerr on your system, then report this to bug-gnulib."
^~~~~
make[3]: *** [Makefile:1895: fseterr.o] Error 1
make[3]: *** Waiting for unfinished jobs....
make[3]: Leaving directory '/home/sbh/foam/foam-extend-4.0/ThirdParty/rpmBuild/BUILD/bison-2.7/lib'
make[2]: *** [Makefile:1651: all] Error 2
make[2]: Leaving directory '/home/sbh/foam/foam-extend-4.0/ThirdParty/rpmBuild/BUILD/bison-2.7/lib'
make[1]: *** [Makefile:1532: all-recursive] Error 1
make[1]: Leaving directory '/home/sbh/foam/foam-extend-4.0/ThirdParty/rpmBuild/BUILD/bison-2.7'
make: *** [Makefile:1462: all] Error 2
error: Bad exit status from /home/sbh/foam/foam-extend-4.0/ThirdParty/rpmBuild/tmp/rpm-tmp.H2roMJ (%build)
RPM build errors:
Bad exit status from /home/sbh/foam/foam-extend-4.0/ThirdParty/rpmBuild/tmp/rpm-tmp.H2roMJ (%build)
Installing package: bison-2.7
Uninstalling bison-2.7 using RPM: bison-2.7-linux64GccDPOpt.x86_64
Installing bison-2.7 using RPM file: /home/sbh/foam/foam-extend-4.0/ThirdParty/rpmBuild/RPMS/x86_64/bison-2.7-linux64GccDPOpt.x86_64.rpm
error: open of /home/sbh/foam/foam-extend-4.0/ThirdParty/rpmBuild/RPMS/x86_64/bison-2.7-linux64GccDPOpt.x86_64.rpm failed: No such file or directory
Done installing package
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May 26, 2019, 16:57
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update: attempt after fresh git pull (link to logs [can view online] - too big ?)
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#2 |
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New Member
bret
Join Date: May 2019
Posts: 7
Rep Power: 7 |
Another edit (3rd) - I deleted all and started over, with trying a prefs.sh file from a similar case on cfd-online. The log file, from
Code:
./Allwmake.firstInstall > log.make 2>&1 ================================================== = Hello, I have a Debian Testing machine, Code:
Linux sbh 4.19.0-5-amd64 #1 SMP Debian 4.19.37-3 (2019-05-15) x86_64 GNU/Linux https://openfoamwiki.net/index.php/I...oam-extend-4.0 and some ideas from questions posted on cfd online; foam-extend-4.0 install not as root How to install foam-extend 4.0 in UBUNTU 18.04 Additionally, I modified the prefs.sh file (attached), and the AllMake.pre and the Allwmake.firstInstall files by simply adding on the same logging instructions I had seen wyldckat use - something like ./Allwmake > $WM_THIRD_PARTY_DIR/logfile 2>&1. It was for my own purposes because I thought it might make it easier to find the problem, especially since I have tried 'stepping through' the make files manually. I started deleting the folder foam-extend-4.0 each time because even after using Allclean, I would find errors in different places, e.g. wmake libso finiteVolume "area" had a 'bad bool casting' complaint, or I would have some problems with gcc49. I also saw confusing (to me at least) things like this in the output logs (attached), Code:
../../gcc/defaults.h:126:24: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
fprintf ((FILE), ","HOST_WIDE_INT_PRINT_UNSIGNED",%u\n", \
^
cfns.gperf:26:14: warning: inline function 'const char* libc_name_p(const char*, unsigned int)' used but never defined
make[3]: *** [Makefile:1058: cp/except.o] Error 1
make[3]: *** Waiting for unfinished jobs....
rm gcc.pod
make[3]: Leaving directory '/home/sbh/foam/foam-extend-4.0/ThirdParty/rpmBuild/BUILD/gcc-4.9.2/objBuildDir/gcc'
make[2]: *** [Makefile:4234: all-stage1-gcc] Error 2
make[2]: Leaving directory '/home/sbh/foam/foam-extend-4.0/ThirdParty/rpmBuild/BUILD/gcc-4.9.2/objBuildDir'
make[1]: *** [Makefile:22967: stage1-bubble] Error 2
make[1]: Leaving directory '/home/sbh/foam/foam-extend-4.0/ThirdParty/rpmBuild/BUILD/gcc-4.9.2/objBuildDir'
make: *** [Makefile:901: all] Error 2
error: Bad exit status from /home/sbh/foam/foam-extend-4.0/ThirdParty/rpmBuild/tmp/rpm-tmp.gjhR8W (%build)
RPM build errors:
Bad exit status from /home/sbh/foam/foam-extend-4.0/ThirdParty/rpmBuild/tmp/rpm-tmp.gjhR8W (%build)
Installing package: gcc-4.9.2
Uninstalling gcc-4.9.2 using RPM: gcc-4.9.2-linux64Gcc49DPOpt.x86_64
Installing gcc-4.9.2 using RPM file: /home/sbh/foam/foam-extend-4.0/ThirdParty/rpmBuild/RPMS/x86_64/gcc-4.9.2-linux64Gcc49DPOpt.x86_64.rpm
error: open of /home/sbh/foam/foam-extend-4.0/ThirdParty/rpmBuild/RPMS/x86_64/gcc-4.9.2-linux64Gcc49DPOpt.x86_64.rpm failed: No such file or directory
Done installing package
Building cmake 3.2.2
Package name : cmake-3.2.2
Package URL : http://www.cmake.org/files/v3.2/cmake-3.2.2.tar.gz
I had some problems attaching files due to size (just the src/Allwmake file gzipped is at 357kB - I really hope my amendments to the 2 make files didn't cause these to be too big, i.e. over 195.3kB - so here is a box.com link to view/download the files: https://app.box.com/s/dn5yh2074e4hgly9harjpmfz92ztnicr - I would fix this issue if I knew how. ), and also it seems to help (for me) to break it down some, so I added a couple additions to the two files Allwmake.firstInstall; Code:
# wmake is required for subsequent targets
( cd wmake/src && make > $WM_PROJECT_DIR/log.wmake.src 2>&1 )
# build ThirdParty sources
( cd $WM_THIRD_PARTY_DIR && ./AllMake.pre > $WM_PROJECT_DIR/log.AllMake.pre 2>&1 )
# We make sure the ThirdParty packages environment variables are up-to-date
# before compiling the rest of OpenFOAM
. $WM_PROJECT_DIR/etc/settings.sh
# build OpenFOAM libraries and applications
src/Allwmake > $WM_PROJECT_DIR/log.src.Allwmake 2>&1
applications/Allwmake > $WM_PROJECT_DIR/log.applications.Allwmake 2>&1
if [ "$1" = doc ]
then
doc/Allwmake
fi
# build ThirdParty sources that depend on main installation
export WM_NCOMPPROCS=1
( cd $WM_THIRD_PARTY_DIR && ./AllMake.post > $WM_PROJECT_DIR/log.AllMake.post 2>&1 )
Code:
# Running stage 1 ./AllMake.stage1 > $WM_PROJECT_DIR/log.AllMake.stage1 2>&1 # Running stage 2 ./AllMake.stage2 > $WM_PROJECT_DIR/log.AllMake.stage2 2>&1 # Running stage 3 ./AllMake.stage3 > $WM_PROJECT_DIR/log.AllMake.stage3 2>&1 # Running stage 4 ./AllMake.stage4 > $WM_PROJECT_DIR/log.AllMake.stage4 2>&1 As mentioned earlier, I am amenable to starting over and following anyone's suggestions. Thank you Last edited by brett1; May 27, 2019 at 12:26. Reason: having problems uploading files due to size |
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June 3, 2019, 18:21
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Started over with a few modifications
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#3 |
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New Member
bret
Join Date: May 2019
Posts: 7
Rep Power: 7 |
Here is my **prefs.sh** file (the only changes from the example version):
(I tried many different bison until i had no error, and between the bounds of 2.4 & <3) Code:
export QT_BIN_DIR=/usr/bin/ export WM_THIRD_PARTY_USE_BISON_24=1 Code:
# Load bison
# ~~~~~~~~~~
#[ -z "$BISON_SYSTEM" ] && [ ! -z $WM_THIRD_PARTY_USE_BISON_27 ] && [ -e $WM_THIRD_PARTY_DIR/packages/bison-$
# _foamSource $WM_THIRD_PARTY_DIR/packages/bison-2.7/platforms/$WM_OPTIONS/etc/bison-2.7.sh
#}
#[ "$FOAM_VERBOSE" -a "$PS1" ] && echo " BISON_DIR is initialized to: $BISON_DIR"
# Load bison
# ~~~~~~~~~~
[ -z "$BISON_SYSTEM" ] && [ ! -z $WM_THIRD_PARTY_USE_BISON_24 ] && [ -e $WM_THIRD_PARTY_DIR/packages/bison-2$
_foamSource $WM_THIRD_PARTY_DIR/packages/bison-2.4/platforms/$WM_OPTIONS/etc/bison-2.4.sh
}
[ "$FOAM_VERBOSE" -a "$PS1" ] && echo " BISON_DIR is initialized to: $BISON_DIR"
and my **AllMake.stage1** has changes; Code:
# bison 2.7
#
[ ! -z "$WM_THIRD_PARTY_USE_BISON_27" ] && {
echo "Building bison 2.7"
# You need a recent version of m4 in order to compile a recent version of bison
( rpm_make -p bison-2.7 -s bison-2.7.spec -u http://ftpmirror.gnu.org/bison/bison-2.7.tar.gz )
}
# bison 2.4
#
[ ! -z "$WM_THIRD_PARTY_USE_BISON_24" ] && {
echo "Building bison 2.4 fool!"
( rpm_make -p bison-2.4 -s bison-2.4.spec -u http://ftpmirror.gnu.org/bison/bison-2.4.tar.gz )
}
Code:
sbh@sbh:~/foam/foam-extend-4.0/src$ wmakeLnInclude foam
sbh@sbh:~/foam/foam-extend-4.0/src$ wmakeLnInclude meshTools/
sbh@sbh:~/foam/foam-extend-4.0/src$ wmakeLnInclude OSspecific//$WM_OSTYPE
sbh@sbh:~/foam/foam-extend-4.0/src$ wmake libso OSspecific/$WM_OSTYPE
'/home/sbh/foam/foam-extend-4.0/lib/linux64GccDPOpt/libOSspecific.so' is up to date.
sbh@sbh:~/foam/foam-extend-4.0/src$ wmake libso foam
SOURCE=global/global.Cver ; sed -e 's/VERSION_STRING/4.0/' -e 's/BUILD_STRING/4.0-268bb07d15d8/' $SOURCE > Make/linux64GccDPOpt/global.C; g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3 -DNoRepository -ftemplate-depth-200 -DOMPI_SKIP_MPICXX -I/home/sbh/foam/foam-extend-4.0/ThirdParty/packages/openmpi-1.8.8/platforms/linux64GccDPOpt/include -I/home/sbh/foam/foam-extend-4.0/ThirdParty/zlib-1.2.3 -IlnInclude -I. -I/home/sbh/foam/foam-extend-4.0/src/foam/lnInclude -I/home/sbh/foam/foam-extend-4.0/src/OSspecific/POSIX/lnInclude -fPIC -c Make/linux64GccDPOpt/global.C -o Make/linux64GccDPOpt/global.o
'/home/sbh/foam/foam-extend-4.0/lib/linux64GccDPOpt/libfoam.so' is up to date.
sbh@sbh:~/foam/foam-extend-4.0/src$ decompositionMethods/AllwmakeLnInclude
+ wmakeLnInclude decompositionMethods
+ wmakeLnInclude metisDecomp
+ wmakeLnInclude parMetisDecomp
+ wmakeLnInclude scotchDecomp
sbh@sbh:~/foam/foam-extend-4.0/src$ ls decompositionMethods/
Allwmake AllwmakeLnInclude decompositionMethods metisDecomp parMetisDecomp scotchDecomp
sbh@sbh:~/foam/foam-extend-4.0/src$ cat decompositionMethods/Allwmake
#!/bin/sh
cd ${0%/*} || exit 1 # run from this directory
set -x
wmakeLnInclude decompositionMethods
wmake libso decompositionMethods
wmake libso metisDecomp
wmake libso parMetisDecomp
wmake libso scotchDecomp
# ----------------------------------------------------------------- end-of-file
sbh@sbh:~/foam/foam-extend-4.0/src$ cd decompositionMethods/
sbh@sbh:~/foam/foam-extend-4.0/src/decompositionMethods$ wmake libso decompositionMethods/
'/home/sbh/foam/foam-extend-4.0/lib/linux64GccDPOpt/libdecompositionMethods.so' is up to date.
sbh@sbh:~/foam/foam-extend-4.0/src/decompositionMethods$ wmake libso metisDecomp/
'/home/sbh/foam/foam-extend-4.0/lib/linux64GccDPOpt/libmetisDecomp.so' is up to date.
sbh@sbh:~/foam/foam-extend-4.0/src/decompositionMethods$ wmake libso parMetisDecomp/
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 -I/home/sbh/foam/foam-extend-4.0/ThirdParty/packages/openmpi-1.8.8/platforms/linux64GccDPOpt/include -I -I../decompositionMethods/lnInclude -I../metisDecomp/lnInclude -I../scotchDecomp/lnInclude -IlnInclude -I. -I/home/sbh/foam/foam-extend-4.0/src/foam/lnInclude -I/home/sbh/foam/foam-extend-4.0/src/OSspecific/POSIX/lnInclude -fPIC -c $SOURCE -o Make/linux64GccDPOpt/parMetisDecomp.o
In file included from parMetisDecomp.C:26:0:
parMetisDecomp.H:38:10: fatal error: decompositionMethod.H: No such file or directory
#include <decompositionMethod.H>
^~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make: *** [parMetisDecomp.dep:342: Make/linux64GccDPOpt/parMetisDecomp.o] Error 1
Code:
# Decomposition methods needed by meshTools decompositionMethods/AllwmakeLnInclude decompositionMethods/Allwmake Code:
sbh@sbh:~/foam/foam-extend-4.0/src/decompositionMethods$ grep -nw ~/foam/log.src.Allwmake -e "Error" -C 20 3407-Making dependency list for source file hierarchGeomDecomp/hierarchGeomDecomp.C 3408-Making dependency list for source file simpleGeomDecomp/simpleGeomDecomp.C 3409-Making dependency list for source file patchConstrainedDecomp/patchConstrainedDecomp.C 3410-SOURCE=decompositionMethod/decompositionMethod.C ; g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3 -DNoRepository -ftemplate-depth-200 -IlnInclude -I. -I/home/sbh/foam/foam-extend-4.0/src/foam/lnInclude -I/home/sbh/foam/foam-extend-4.0/src/OSspecific/POSIX/lnInclude -fPIC -c $SOURCE -o Make/linux64GccDPOpt/decompositionMethod.o 3411-SOURCE=manualDecomp/manualDecomp.C ; g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3 -DNoRepository -ftemplate-depth-200 -IlnInclude -I. -I/home/sbh/foam/foam-extend-4.0/src/foam/lnInclude -I/home/sbh/foam/foam-extend-4.0/src/OSspecific/POSIX/lnInclude -fPIC -c $SOURCE -o Make/linux64GccDPOpt/manualDecomp.o 3412-SOURCE=geomDecomp/geomDecomp.C ; g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3 -DNoRepository -ftemplate-depth-200 -IlnInclude -I. -I/home/sbh/foam/foam-extend-4.0/src/foam/lnInclude -I/home/sbh/foam/foam-extend-4.0/src/OSspecific/POSIX/lnInclude -fPIC -c $SOURCE -o Make/linux64GccDPOpt/geomDecomp.o 3413-SOURCE=simpleGeomDecomp/simpleGeomDecomp.C ; g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3 -DNoRepository -ftemplate-depth-200 -IlnInclude -I. -I/home/sbh/foam/foam-extend-4.0/src/foam/lnInclude -I/home/sbh/foam/foam-extend-4.0/src/OSspecific/POSIX/lnInclude -fPIC -c $SOURCE -o Make/linux64GccDPOpt/simpleGeomDecomp.o 3414-SOURCE=hierarchGeomDecomp/hierarchGeomDecomp.C ; g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3 -DNoRepository -ftemplate-depth-200 -IlnInclude -I. -I/home/sbh/foam/foam-extend-4.0/src/foam/lnInclude -I/home/sbh/foam/foam-extend-4.0/src/OSspecific/POSIX/lnInclude -fPIC -c $SOURCE -o Make/linux64GccDPOpt/hierarchGeomDecomp.o 3415-SOURCE=patchConstrainedDecomp/patchConstrainedDecomp.C ; g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3 -DNoRepository -ftemplate-depth-200 -IlnInclude -I. -I/home/sbh/foam/foam-extend-4.0/src/foam/lnInclude -I/home/sbh/foam/foam-extend-4.0/src/OSspecific/POSIX/lnInclude -fPIC -c $SOURCE -o Make/linux64GccDPOpt/patchConstrainedDecomp.o 3416-'/home/sbh/foam/foam-extend-4.0/lib/linux64GccDPOpt/libdecompositionMethods.so' is up to date. 3417-+ wmake libso metisDecomp 3418-wmakeLnInclude: linking include files to ./lnInclude 3419-Making dependency list for source file metisDecomp.C 3420-could not open file metis.h for source file metisDecomp.C 3421-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../decompositionMethods/lnInclude -I../scotchDecomp/lnInclude -IlnInclude -I. -I/home/sbh/foam/foam-extend-4.0/src/foam/lnInclude -I/home/sbh/foam/foam-extend-4.0/src/OSspecific/POSIX/lnInclude -fPIC -c $SOURCE -o Make/linux64GccDPOpt/metisDecomp.o 3422-In file included from metisDecomp.C:26:0: 3423-metisDecomp.H:38:10: fatal error: decompositionMethod.H: No such file or directory 3424- #include "decompositionMethod.H" 3425- ^~~~~~~~~~~~~~~~~~~~~~~ 3426-compilation terminated. 3427:make: *** [metisDecomp.dep:319: Make/linux64GccDPOpt/metisDecomp.o] Error 1 3428-+ wmake libso parMetisDecomp 3429-wmakeLnInclude: linking include files to ./lnInclude 3430-Making dependency list for source file parMetisDecomp.C 3431-could not open file parmetis.h for source file parMetisDecomp.C 3432-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 -I/home/sbh/foam/foam-extend-4.0/ThirdParty/packages/openmpi-1.8.8/platforms/linux64GccDPOpt/include -I -I../decompositionMethods/lnInclude -I../metisDecomp/lnInclude -I../scotchDecomp/lnInclude -IlnInclude -I. -I/home/sbh/foam/foam-extend-4.0/src/foam/lnInclude -I/home/sbh/foam/foam-extend-4.0/src/OSspecific/POSIX/lnInclude -fPIC -c $SOURCE -o Make/linux64GccDPOpt/parMetisDecomp.o 3433-In file included from parMetisDecomp.C:26:0: 3434-parMetisDecomp.H:37:10: fatal error: decompositionMethod.H: No such file or directory 3435- #include "decompositionMethod.H" 3436- ^~~~~~~~~~~~~~~~~~~~~~~ 3437-compilation terminated. 3438:make: *** [parMetisDecomp.dep:342: Make/linux64GccDPOpt/parMetisDecomp.o] Error 1 3439-+ wmake libso scotchDecomp 3440-wmakeLnInclude: linking include files to ./lnInclude 3441-Making dependency list for source file scotchDecomp/scotchDecomp.C 3442-Making dependency list for source file engineScotchDecomp/engineScotchDecomp.C 3443-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/home/sbh/foam/foam-extend-4.0/ThirdParty/packages/scotch-6.0.4/platforms/linux64GccDPOpt/include -I../decompositionMethods/lnInclude -IlnInclude -I. -I/home/sbh/foam/foam-extend-4.0/src/foam/lnInclude -I/home/sbh/foam/foam-extend-4.0/src/OSspecific/POSIX/lnInclude -fPIC -c $SOURCE -o Make/linux64GccDPOpt/scotchDecomp.o 3444-SOURCE=engineScotchDecomp/engineScotchDecomp.C ; g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3 -DNoRepository -ftemplate-depth-200 -I/home/sbh/foam/foam-extend-4.0/ThirdParty/packages/scotch-6.0.4/platforms/linux64GccDPOpt/include -I../decompositionMethods/lnInclude -IlnInclude -I. -I/home/sbh/foam/foam-extend-4.0/src/foam/lnInclude -I/home/sbh/foam/foam-extend-4.0/src/OSspecific/POSIX/lnInclude -fPIC -c $SOURCE -o Make/linux64GccDPOpt/engineScotchDecomp.o 3445-'/home/sbh/foam/foam-extend-4.0/lib/linux64GccDPOpt/libscotchDecomp.so' is up to date. 3446-+ wmake libso lagrangian/basic 3447-wmakeLnInclude: linking include files to ./lnInclude 3448-Making dependency list for source file passiveParticle/passiveParticleCloud.C 3449-Making dependency list for source file indexedParticle/indexedParticleCloud.C 3450-SOURCE=passiveParticle/passiveParticleCloud.C ; g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3 -DNoRepository -ftemplate-depth-200 -IlnInclude -I. -I/home/sbh/foam/foam-extend-4.0/src/foam/lnInclude -I/home/sbh/foam/foam-extend-4.0/src/OSspecific/POSIX/lnInclude -fPIC -c $SOURCE -o Make/linux64GccDPOpt/passiveParticleCloud.o 3451-SOURCE=indexedParticle/indexedParticleCloud.C ; g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3 -DNoRepository -ftemplate-depth-200 -IlnInclude -I. -I/home/sbh/foam/foam-extend-4.0/src/foam/lnInclude -I/home/sbh/foam/foam-extend-4.0/src/OSspecific/POSIX/lnInclude -fPIC -c $SOURCE -o Make/linux64GccDPOpt/indexedParticleCloud.o 3452-'/home/sbh/foam/foam-extend-4.0/lib/linux64GccDPOpt/liblagrangian.so' is up to date. 3453-+ wmake libso edgeMesh 3454-wmakeLnInclude: linking include files to ./lnInclude 3455-Making dependency list for source file edgeMesh.C 3456-Making dependency list for source file edgeMeshIO.C 3457-Making dependency list for source file featureEdgeMesh.C 3458-SOURCE=edgeMesh.C ; g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3 -DNoRepository -ftemplate-depth-200 -IlnInclude -I. -I/home/sbh/foam/foam-extend-4.0/src/foam/lnInclude -I/home/sbh/foam/foam-extend-4.0/src/OSspecific/POSIX/lnInclude -fPIC -c $SOURCE -o Make/linux64GccDPOpt/edgeMesh.o Thank you. PS. I also changed the url to pull parmetis-3.0.4.tar.gz. as the umn.edu site was down. Hope this isn't the source of the error, but the ubuntu package repository says it is the "original"... https://www.isitdownrightnow.com/gla...c.umn.edu.html From **AllMake.stage3**; Code:
# ParMetis
if [ -z "$PARMETIS_SYSTEM" ]
then
# ParMetis 4.0.3
#
[ ! -z "$WM_THIRD_PARTY_USE_PARMETIS_403" ] && {
echo "Building ParMetis 4.0.3"
( rpm_make -p parmetis-4.0.3 -s parmetis-4.0.3.spec -u http://archive.ubuntu.com/ubuntu/pool/multive$
# ( rpm_make -p parmetis-4.0.3 -s parmetis-4.0.3.spec -u http://glaros.dtc.umn.edu/gkhome/fetch/sw/par$
}
else
echo "Using system installed ParMetis"
echo ""
fi
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June 7, 2019, 19:31
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#4 |
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Retired Super Moderator
Bruno Santos
Join Date: Mar 2009
Location: Lisbon, Portugal
Posts: 10,982
Blog Entries: 45
Rep Power: 128  |
Greetings brett1,
 Wow, that's a hell of a fight! I didn't study what you've done specifically so far, but I'll address at least the latest post.And I have no idea if GCC 8 can be used with foam-extend 4.0 or not, but I believe that foam-extend 4.1 (which is development) should be compatible with it... but first let's hold off on that... ... Because the "src" folder seems to have built mostly without errors. Even if Scotch and Metis are not compiled, you can still mostly use foam-extend 4.0 as it is right now, namely if you proceed with building the "applications" folder and build the rest. The downside is having to use the other less dynamic decomposition methods, such as "simple" and "hierarchical"... The problem with "stage3" is essentially this: Code:
error: unpacking of archive failed on file /usr/lib/.build-id: cpio: mkdir failed - Inappropriate ioctl for device Please try using the following commands to unpack said TGZ files: Code:
cd $WM_THIRD_PARTY for file in rpmBuild/TGZS/x86_64/*.tgz; do tar -xf $file; done Code:
source $WM_PROJECT_DIR/etc/bashrc Code:
foam ./Allwmake > log.make 2>&1 If by any chance you want to try and build the ongoing development version 4.1, then run: Code:
cd ~ mkdir foam cd foam git clone git://git.code.sf.net/p/foam-extend/foam-extend-4.1 foam-extend-4.1 cd foam-extend-4.1 git checkout nextRelease Best regards, Bruno
__________________
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June 15, 2019, 13:35
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resolved foam-extend-4.0 & 4.1 on Debian Testing
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#5 |
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New Member
bret
Join Date: May 2019
Posts: 7
Rep Power: 7 |
Hello and apologies for the delay - i can only work on this on weekends.
So summarily, the prescription that Bruno suggested worked fine - on both 4.0 & 4.1. There were some PyFoam associated SyntaxError but so far the first example works fine. It is noteworthy that the 4.1 version has this exact error: https://www.cfd-online.com/Forums/op...ary-print.html and it was easily resolved by (my only attempt) adding the pFinal{} to the system/fvSolution file. I have not studied foam enough to begin to understand why this error occurs but not in 4.0. Hopefully errors for future examples or my own work will be as easily resolved. Here is the modified system/fvSolution file; Code:
/*--------------------------------*- C++ -*----------------------------------*\
2 | ========= | |
3 | \\ / F ield | foam-extend: Open Source CFD |
4 | \\ / O peration | Version: 4.1 |
5 | \\ / A nd | Web: http://www.foam-extend.org |
6 | \\/ M anipulation | |
7 \*---------------------------------------------------------------------------*/
8 FoamFile
9 {
10 version 2.0;
11 format ascii;
12 class dictionary;
13 object fvSolution;
14 }
15 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
16
17 solvers
18 {
19 p
20 {
21 solver PCG;
22 preconditioner DIC;
23 tolerance 1e-06;
24 relTol 0;
25 }
26
27 pFinal
28 {
29 solver PCG;
30 preconditioner DIC;
31 tolerance 1e-06;
32 relTol 0;
33 }
34
35 U
36 {
37 solver BiCGStab;
38 preconditioner DILU;
39 tolerance 1e-05;
40 relTol 0;
41 }
42 }
43
44 PISO
45 {
46 nCorrectors 2;
47 nNonOrthogonalCorrectors 0;
48 pRefCell 0;
49 pRefValue 0;
50 }
51
52
53 // ************************************************************************* //
54
Thanks again Bruno! PS log... & log2... are only up to leaving the ThirdParty work, before and after Bruno's prescription. log3... is the complete Allwmake.firstInstall PPS I did install gcc-7 and friends - from oldstable |
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June 16, 2019, 05:14
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Install FOAM-extend-4.1 (actually nextRelease branch of 4.0)
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#6 |
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Member
Saleh Abuhanieh
Join Date: Nov 2017
Posts: 83
Rep Power: 9 |
Hi,
I will recommend the below installation guide prepared by Chalmers university: https://pingpong.chalmers.se/public/...o?item=4764601 Regards, Last edited by wyldckat; June 16, 2019 at 15:33. Reason: corrected link |
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June 16, 2019, 15:39
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#7 | ||
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Retired Super Moderator
Bruno Santos
Join Date: Mar 2009
Location: Lisbon, Portugal
Posts: 10,982
Blog Entries: 45
Rep Power: 128 |
Quick answers:
Quote:
Quote:
The only thing that wasn't build was swak4Foam, but that is likely because Mercurial (Hg) wasn't installed. But it's only needed if you're planning on using swak4Foam.
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June 16, 2019, 17:47
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swaq4Foam
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#8 |
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New Member
bret
Join Date: May 2019
Posts: 7
Rep Power: 7 |
Hello,
Thanks for looking at it again! I actually do have mercurial installed.... 4.8.2-1. (not sure of this .hg file yet...) I am interested in using that library so, since it is in ThirdParty I think I'll get the source in tgz format and try your trick again. I'll post my attempts and hopefully positive result, Thanks, Brett EDIT I notice from AllMake.stage5 that it pulls a clone, not a tgz for swaq4Foam. Anyways, will post soonish... Last edited by brett1; June 16, 2019 at 23:33. Reason: clarification |
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June 17, 2019, 00:01
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swaq4Foam
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#9 |
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New Member
bret
Join Date: May 2019
Posts: 7
Rep Power: 7 |
Hello again,
Apparently (maybe a Debian thing) mercurial didn't have the "server" packages installed, just a "bin" and "common"... So the only errors I saw were two regarding something 'HUGE' - here it is in the log file at around line 2350 & 2353. Haven't spent much time seeing if it is of concern yet... ? Code:
Objects/unitCylinderSearchableSurface.C: In member function ‘void Foam::unitCylinderSearchableSurface::findLineAll(const point&, const point&, Foam::List<Foam::PointIndexHit<Foam::Vector<double> > >&) const’:
Objects/unitCylinderSearchableSurface.C:129:27: error: ‘HUGE’ was not declared in this scope
mag(topIntersect)>HUGE
^~~~
Objects/unitCylinderSearchableSurface.C:141:30: error: ‘HUGE’ was not declared in this scope
mag(bottomIntersect)>HUGE
^~~~
make: *** [Objects/unitCylinderSearchableSurface.dep:282: Make/linux64GccDPInt32Opt/unitCylinderSearchableSurface.o] Error 1
wmakeLnInclude: linking include files to ./lnInclude
Thanks Brett |
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September 30, 2019, 23:36
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#10 | |
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New Member
Xiangjie Wang
Join Date: Jul 2019
Posts: 26
Rep Power: 7 |
Quote:
Problems on installing Foam-extend 4.0/ swak4Foam on ubuntu18.0.4 This is what gschaider replied. I hope it will be helpful. Best wishes. Xiangjie |
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| Tags |
| foam-extend-4.0, gnu |
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