[overture] Re: after install then check only part success (overture 2.5 on ubuntu 12.04 lts 64bit)
- From: "Wang Jianliang" <hustwjl@xxxxxxxxx>
- To: overture <overture@xxxxxxxxxxxxx>
- Date: Fri, 5 Apr 2013 20:48:48 +0800
now I check it mp is ok now, and the whole cg
I share the steps to install it with Ubuntu 12.04 LTS
Steps Taken to install Overture on Windows using VirtualBoxVM
follow the work by Christopher Jarvis - chjarvis@xxxxxx
updated to ubuntu 12.04.1 by Jianliang Wang - hustwjl@xxxxxxxxx
by Jarvis September 20, 2012
by Jianliang Wang 2013-4-5 19:58:41
Install VM and Linux
1. Install VirtualBox
(a) download from https://www.virtualbox.org/
2. Set up VM and install OS
(a) Ubuntu 12.04.1 LTS (64 bit, desktop)
Install Overture on VM
To install Overture in Ubuntu Jarvis followed the instructions of Mohammad
Abouali found here:
http://mabouali.wordpress.com/2012/01/16/installing-overture-on-a-freshly-installed-ubuntu/
and ref
http://www.overtureframework.org/documentation/Installing_Overture_on_Ubuntu_10_04_LTS.pdf
I can not access the wordpress.com, so I followed the pdf
the change most in the square brackets "[...]"
1. Begin with fresh install of Ubuntu 12.04.1 LTS
(a) update all packages(I do not update)
(b) install
i. install tcsh [the command on official guide is used this, I think, not the
bash shell,when you type the command, first enter tcsh by type tcsh]
sudo apt-get install tcsh
ii. emacs [you can use the gedit, I like it]
(c) set default current folder in path [ add the current, you need this for
check.p or other files]
i. set path = (. ~/bin /usr/apps/bin $path)
(d) reboot
2. Prelimenary packages
(a) sudo apt-get install build-essential manpages-dev gfortran autoconf automake
(b) check compiler versions
i. gcc - 4.6.3
ii. g++ - 4.6.3
iii. gfortran - 4.6.3
3. OpenMotif
(a) install
i. libmotif4 [not libmotif3]
ii. libmotif-dev (depends on libmotif4)
[sudo apt-get install libmotif4 libmotif-dev]
4. OpenGL and Mesa
(a) sudo apt-get install libgl1-mesa-dev libglu1-xorg libglu1-xorg-dev libglut3
libglut3-dev x11proto-gl-dev
x11proto-print-dev libjpeg62-dev libzip-dev libperl-dev libXpm-dev libXp-dev
libxmu-dev libxi-dev
[no libglu1-xorg and libglu1-xorg-dev]
[there some should change to:
sudo apt-get install libgl1-mesa-glx libgl1-mesa-dev freeglut3 freeglut3-dev
x11proto-gl-dev x11proto-print-dev libjpeg62-dev libzip-dev libperl-dev
libXpm-dev libXp-dev libxmu-dev libxi-dev
]
From here I used downloaded the tar files and extracted to and installed in
“~/apps/<PACKAGE>”. Note: the
commands are run from the extracted package directory.
1. HDF5 (hdf5-1.6.9)
(a) sudo ln -s make gmake (symbolic link to gmake from make)
(b) unsetenv CC
(c) unsetenv cc
(d) setenv CC gcc
(e) ./configure -prefix=`pwd`
(f) make
(g) make install
2. A++ (A++P++-0.8.0)
(a) I extracted to ~/apps/A++P++-0.8.0
(b) configure -enable-SHARED_LIBS -prefix `pwd`
(c) make
(d) make install
(e) make check
2
3. LAPACK ([lapack-3.4.2])
(a) cp make.inc.example make.inc
(b) make blaslib lapacklib tmglib
(c) cp librefblas.a libblas.a
4. PETSc ([2.3.2-p6 lite])
(a) setenv PETSC_DIR `pwd`
(b) ./config/configure.py -with-debugging=0 -with-fortran=0 -with-matlab=0
-with-mpi=0 -with-shared=1
-with-dynamic=1 -prefix=`pwd` -download-c-blas-lapack=1
(c) setenv PETSC_ARCH “recommended”
(d) make all
(e) make install (may not be necessary install dir is make dir)
(f) make test
(g) reboot
5. Overture (Overture.v25)
(a) set up defenv [ a file in Overture directory]
i. setenv XLIBS /usr
ii. setenv MOTIF /usr
iii. setenv OpenGL /usr
iv. setenv HDF ~/apps/hdf5-1.6.9
v. setenv APlusPlus ~/apps/A++P++-0.8.0/A++/install
vi. setenv Overture ~/apps/Overture.v25
vii. setenv CG ~/apps/cg.v25
viii. setenv LAPACK ~/apps/lapack-3.4.2
[ remember to comment the not needed enviorment]
(b) source defenv
[ and you should to mk dir in the apps directory, link the OpenGL and lib64
directory to the right position, you can use locate to find the gl.h
[/usr/include/GL/gl.h
] and the [/usr/lib/x86_64-linux-gnu/] libGL.so ]
(c) in configure file change $FortranDouble to $FortranDouble =
"-fdefault-real-8 -fdefault-double-8"; (prevents error during cg compile)
(d) ** IF you are going to install cg then correct
cg.v25/sm/src/getRayleighSpeed.C before compliling **
change: printf(getRayleighSpeed: mu=%e, lambda=%e,
rho=%e\n",mu,lambda,rho,gamma);
to: cout < < "getRayleighSpeed: mu= "< < mu < < ", lambda="< < lambda < <",
rho=" < < rho < < ",
gamma= " < < gamma < < endl;
and have other files , which you should have to [a (const char*) :]
like (const char*)userKnownSolution);
which file you should change you can follow the compile warning
(e) configure
(f) make (or make -j# for parallel using # cores)
(g) check.p (all successful)
6. cg (cg.v25)
(a) make
(b) make check
[not all successful]
follow this two to change
mp error
//www.freelists.org/post/overture/after-install-then-check-only-part-success-overture-25-on-ubuntu-1204-lts-64bit,5
7. Install complete!!
8. Test
(a) create local test folder
(b) copy cilc.cmd from Overture.v25/sampleGrids to test folder
(c) copy cylinder.cmd from cg.v25/ins/cmd to test folder
(d) cd to test folder
(e) ogen cilc (generates default grid)
(f) cgins cylinder (solves PDE)
I do not remember all the details, if have problem, feedback this
Wang Jianliang
from： Bill Henshaw
send time： 2013-04-04 23:19
Email to： overture
subject： [overture] Re: after install then check only part success (overture
2.5 on ubuntu 12.04 lts 64bit)
Hi Janlinag,
From the output file I see the mistake is shown on the last line:
$ad2=0; ad21=0; $ad22=0.; $adcBoussinesq=0.;
The variable ad21 should be $ad21 (perl variable).
You will need to change line 128 of cg/mp/cmd/twoDomain.cmd to (note $ad21)
$ad2=0; $ad21=0; $ad22=0.; $adcBoussinesq=0.;
Thanks for reporting this bug.
...Bill
P.S. Your run "by hand" did not work properly -- this needs to be run from the
cg/mp/check directory I believe.
On 04/03/2013 06:44 PM, Wang Jianliang wrote:
Hi, Bill
I attatch the out file to you, and I also run by hand follow your advice
/home/alljoyland/wjl/cg.v25/mp/bin/cgmp noplot ./../cmd/twoDomain.cmd
-g=twoSquaresInterfacee1.order2.hdf -kappa1=1. -ktc1=1. -kappa2=.1 -ktc2=.1
-tf=.1 -tp=.05 -ts=pc -coupled=1 -tz=poly -degreet1=2 -degreet2=2 -debug=1
-method2=ins -go=go
and get the output :
/home/alljoyland/wjl/cg.v25/mp/bin/cgmp noplot ./../cmd/twoDomain.cmd
-g=twoSquaresInterfacee1.order2.hdf -kappa1=1. -ktc1=1. -kappa2=.1 -ktc2=.1
-tf=.1 -tp=.05 -ts=pc -coupled=1 -tz=poly -degreet1=2 -degreet2=2 -debug=1
-method2=ins -go=go
A++ Internal_Index bounds checking: ON
cgmp: reading commands from file [./../cmd/twoDomain.cmd]
Did not find or could not open the file
/home/alljoyland/wjl/Overture.v25/.overturerc
User commands are being saved in the file `cgmp.cmd'
read command file =./../cmd/twoDomain.cmd
ERROR:unable to open file [./../cmd/twoDomain.cmd] or
[./../cmd/twoDomain.cmd.cmd]
close dialog/
Enter the name of an (old) overlapping grid file or type 'ogen' to generate a
grid:
see the attatchment for more information
Thank you very much!
Wang Jianliang
From： Bill Henshaw
Time： 2013-04-03 23:23
To： overture
Subject： [overture] Re: after install then check only part success (overture
2.5 on ubuntu 12.04 lts 64bit)
Hi Jianliang,
There is probably some mistake in the perl script that isn't being detected
with the version of perl that we use.
To get more information I wonder if you can provide the output file
twoSquareAdInsExp.out
or run the case "by hand" in the cg/mp/check directory:
/home/alljoyland/wjl/cg.v25/mp/bin/cgmp noplot ./../cmd/twoDomain.cmd
-g=twoSquaresInterfacee1.order2.hdf -kappa1=1. -ktc1=1. -kappa2=.1 -ktc2=.1
-tf=.1 -tp=.05 -ts=pc -coupled=1 -tz=poly -degreet1=2 -degreet2=2 -debug=1
-method2=ins -go=go
to see where it fails.
...Bill
On 04/02/2013 08:53 PM, Wang Jianliang wrote:
Sorry for long no reply this post
I have reinstall the overture 2.5 and cg 2.5
and I will share my install experience sometime later
Os : Ubuntu 12.04.1 64 bit desktop
and I have refer
http://www.overtureframework.org/documentation/Installing_Overture_on_Ubuntu_10_04_LTS.pdf
//www.freelists.org/post/overture/Overture-new-v25-released-cgins-errors,4
to modified some error
but something should change for the newer version of ubuntu
now only two errors to check cgmp now
I do not how to debug this perl script
cd cg.v25/mp/check
make check
the error is:
running: /home/alljoyland/wjl/cg.v25/mp/bin/cgmp noplot ./../cmd/twoDomain.cmd
-g=twoSquaresInterfacee1.order2.hdf -kappa1=1. -ktc1=1. -kappa2=.1 -ktc2=.1
-tf=.1 -tp=.05 -ts=pc -coupled=1 -tz=poly -degreet1=2 -degreet2=2 -debug=1
-method2=ins -go=go >! twoSquareAdInsExp.out
Can't modify constant item in scalar assignment at (eval 10) line 1, at EOF
*** There was an error running /home/alljoyland/wjl/cg.v25/mp/bin/cgmp and
generating twoSquareAdInsExp ****
running: /home/alljoyland/wjl/cg.v25/mp/bin/cgmp noplot ./../cmd/twoDomain.cmd
-g=twoSquaresInterfacee1.order2.hdf -kappa1=1. -ktc1=1. -kappa2=.1 -ktc2=.1
-tf=.1 -tp=.02 -dtMax=.02 -ts=im -nc=5 -coupled=0 -tz=poly -degreet1=2
-degreet2=2 -iTol=1.e-9 -debug=1 -method2=ins -go=go >! twoSquareAdInsImp.out
Can't modify constant item in scalar assignment at (eval 10) line 1, at EOF
*** There was an error running /home/alljoyland/wjl/cg.v25/mp/bin/cgmp and
generating twoSquareAdInsImp ****
********************************************************
************ cgmp: There were 2 ERRORS ****************
********************************************************
the whole check log is:
ubuntu:~/wjl/cg.v25/mp/check> make check
ln -sf ../cmd/adDomain.h .
ln -sf ../cmd/cnsDomain.h .
ln -sf ../cmd/insDomain.h .
ln -sf ../cmd/smDomain.h .
ln -sf ../../common/src/check.p .
check.p -solver=cgmp
================================================================================
This perl script will run regression tests
(The lists of tests is in the file named 'tests')
Usage:
check.p [-test=testName] [-replace] [-check=<checkFileDirectory>]
[-solver=name] [-verbose=<num>]
-test=testName : name of a particular test to run (by default do all)
-replace : replace check files with the new ones computed
-verbose : verbose=0 : print very little, verbose=1 print more
==============================================================================
program=CGBUILDPREFIX/mp/bin/cgmp
checkFile=mp.check
Using program = /home/alljoyland/wjl/cg.v25/mp/bin/cgmp
Using the executable: /home/alljoyland/wjl/cg.v25/mp/bin/cgmp
running: /home/alljoyland/wjl/cg.v25/mp/bin/cgmp noplot ./aaTwoSquare >!
aaTwoSquare.out
checkCheckFiles: files mp.check and aaTwoSquare.check agree at 7 times ,
maxDiff=0.00e+00, (tol=1.00e-05)
... "aaTwoSquare" appears to be correct
running: /home/alljoyland/wjl/cg.v25/mp/bin/cgmp noplot ./aaTwoBox >!
aaTwoBox.out
checkCheckFiles: files mp.check and aaTwoBox.check agree at 5 times ,
maxDiff=0.00e+00, (tol=1.00e-05)
... "aaTwoBox" appears to be correct
running: /home/alljoyland/wjl/cg.v25/mp/bin/cgmp noplot ./iaTwoSquare >!
iaTwoSquare.out
checkCheckFiles: files mp.check and iaTwoSquare.check agree at 5 times ,
maxDiff=0.00e+00, (tol=1.00e-05)
... "iaTwoSquare" appears to be correct
running: /home/alljoyland/wjl/cg.v25/mp/bin/cgmp noplot ./../cmd/twoDomain.cmd
-g=twoSquaresInterfacee1.order2.hdf -kappa1=1. -ktc1=1. -kappa2=.1 -ktc2=.1
-tf=.1 -tp=.05 -ts=pc -coupled=1 -tz=poly -degreet1=2 -degreet2=2 -debug=1
-method2=ins -go=go >! twoSquareAdInsExp.out
Can't modify constant item in scalar assignment at (eval 10) line 1, at EOF
*** There was an error running /home/alljoyland/wjl/cg.v25/mp/bin/cgmp and
generating twoSquareAdInsExp ****
running: /home/alljoyland/wjl/cg.v25/mp/bin/cgmp noplot ./../cmd/twoDomain.cmd
-g=twoSquaresInterfacee1.order2.hdf -kappa1=1. -ktc1=1. -kappa2=.1 -ktc2=.1
-tf=.1 -tp=.02 -dtMax=.02 -ts=im -nc=5 -coupled=0 -tz=poly -degreet1=2
-degreet2=2 -iTol=1.e-9 -debug=1 -method2=ins -go=go >! twoSquareAdInsImp.out
Can't modify constant item in scalar assignment at (eval 10) line 1, at EOF
*** There was an error running /home/alljoyland/wjl/cg.v25/mp/bin/cgmp and
generating twoSquareAdInsImp ****
********************************************************
************ cgmp: There were 2 ERRORS ****************
********************************************************
make: *** [check] Error 1
ubuntu:~/wjl/cg.v25/mp/check>
Wang Jianliang
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