Installation on Ubuntu

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Today is 3/29/2010 - These are notes on how to install instructions for flooxs on 64-bit Ubuntu 9.10 Karmic Koala. These instructions are intended for linux/unix beginners. You may email me direct questions about installing flooxs on Ubuntu at nrowsey at ufl.edu, but please try these instructions first.


Get Your Flooxs!

1. Download the software and put it on your hard drive in a directory called flooxs $ mkdir ~/flooxs - go to http://www.flooxs.tec.ufl.edu/download.html, download the latest linux executable file (get the one that says linux)

2. Unpack via double click -> made dir rel2008


3. Get Started: Try to run FLOOXS $ cd ~/flooxs/rel2008 $ FLXSHOME=`pwd` $ cd src $ ./flooxs.new ./flooxs.new: error while loading shared libraries: liblapack.so.3: cannot open shared object file: No such file or directory

4. Get another environment varible, LD_LIBRARY_PATH - swamp3 says: $ setenv LD_LIBRARY_PATH /home/killebrew0/flooxs/linux/support/petsc-2.1.6/lib/ libO_c++/linux:/home/killebrew0/flooxs/linux/lib - so I'll try to find. I found it. I'll set the path to: $ LD_LIBRARY_PATH="/home/nicrawfolerd/flooxs/rel2008/support/petsc-2.3.2-p7/lib/linux-gnu-c-debug" - same error, so $ LD_LIBRARY_PATH="/home/nicrawfolerd/flooxs/rel2008/support/petsc-2.3.2-p7/lib/"

5. Ok, I don't think you have BLAS/LAPACK, so get it using the PETSc stuff: - Download the latest PETSc - put it in $FLXSHOME/support $ cd $FLXSHOME/support $ gunzip -c petsc-3.0.0-p11.tar.gz | tar -xof - $ cd petsc-3.0.0-p11 $ PETSC_DIR=$PWD; export PETSC_DIR

6. Find out how to Configure PETSc, with BLAS, LAPACK, and MPI - check out examples at $PETSC_DIR/config/examples/*.py - eg: linux-gnu-amd64.py


#!/usr/bin/env python

configure_options = [ '--download-mpich=1', '--download-mpich-pm=gforker', '--download-f-blas-lapack=1', '--download-prometheus=1', '--download-parmetis=1', '--with-debugging=0' ]

if __name__ == '__main__': import sys,os sys.path.insert(0,os.path.abspath('config')) import configure configure.petsc_configure(configure_options)

- from website: One can update these files and run as: config/examples/linux-gnu-amd64.py

# Using the bash shell, assuming BLAS, LAPACK, MPICH are not currently installed ./config/configure.py will download & install BLAS, LAPACK, MPICH if they are not already installed on the system) : 

       	export PETSC_DIR=/home/petsc/petsc-3.0.0-p0

cd $PETSC_DIR 

   	    ./config/configure.py --with-cc=gcc --with-fc=gfortran --download-f-blas-lapack=1 --download-mpich=1
   	    make
   	    make test

7. Configure PETSc with BLAS, LAPACK, and MPI 

       	$ cd $FLXSHOME/support/petsc...
       	$ export PETSC_DIR `pwd`

- save a backup: $ cd $PETSC_DIR/config/examples $ cp linux-gnu-amd64.py linux-gnu-amd64.py.bk

- edit linux-gnu-amd64.py to include the BLAS/LAPACK/MPICH install options:

configure_options = [ '--download-mpich=1', '--download-mpich-pm=gforker', '--download-f-blas-lapack=1', '--download-prometheus=1', '--download-parmetis=1', '--with-debugging=0', '--with-cc=gcc', '--with-fc=gfortran', '--download-f-blas-lapack=1', '--download-mpich=1' ]

- specify enviornment variable for bash [can be specified in ~/.bashrc] ($ export PETSC_DIR=/home/balay/petsc-3.0.0-p0) this one you did $ export PETSC_ARCH=linux-gnu-c-debug  ;#do this one now


- configure with this python? script: $ ./config/examples/linux-gnu-amd64.py

7a. Notice: Have to get gfortran and gcc $ sudo apt-get install gfortran $ sudo apt-get install gcc (already had this)


=====================================================================

WARNING! Compiling PETSc with no debugging, this should only be done for timing and production runs. All development should be done when configured using --with-debugging=1

=====================================================================

-ok I think we can ignore this one, we are a production run :)


=====================================================================

Warning: PETSC_ARCH from environment does not match command-line. Warning: Using from command-line: linux-gnu-amd64, ignoring environment: linux-gnu-c-debug

=====================================================================

-ok change PETSC_ARCH to linux-gnu-amd64

2/24/2010 $ cd ~/flooxs/rel2008 $ FLXSHOME=`pwd` $ export FLXSHOME $ cd $FLXSHOME/support/petsc-3.0.0-p11 $ PETSC_DIR=$PWD; export PETSC_DIR $ export PETSC_ARCH=linux-gnu-amd64 $ ./config/examples/linux-gnu-amd64.py

Could not find a C compiler. Please set with the option --with-cxx or -CXX and load the config.compilers module.

try $ sudo apt-get install build-essential seems to have worked with the last message: Compiling Prometheus; this may take several minutes So, now: $ make all $ test all

no errors

8. tk/tcl/blt $ sudo apt-get install tk tcl blt - they might have been installed in /usr/bin - tk seems to be related to wish?

9. SuperLU Debian Packages: http://packages.debian.org/source/sid/superlu $ sudo apt-get install libsuperlu3 $ sudo apt-get install libsuperlu3-dev - I think it's in /usr/lib Website says other pagackges related to superlu, but seem to have them already.

10. UMFpack googled, saw that someone else got umfpack via synaptic. searched synaptic for libumfpack, got a hit. will try $ sudo apt-get install libumfpack (or libumfpack5) (or libumfpack5.4.0) $ sudo apt-get install libumfpack5.4.0  ;# this worked

11. On to FLOOPS/FLOODS - edit library paths - Edit your library paths $ cd $FLXSHOME/arch $ cp linux64 linux64_bk ;# (makes a backup) $ gedit linux64 & - you might need to update locations for your specific versions of the support libraries.

THIS IS FRIKIN HARD :(:(:( for *each* old path name, you have to navigate to that dir in an old flooxs directory, find what files are there, and then find . -name "*file*" -print those files to see where your new ones are. Most of the time they will be .h or .a files.

- TCL/TK/BLT $ find / -name tcl.h - only found it in FLXSHOME/include and FLXSHOME/support/tcl.?.? - note, .h probably means "header"

looked in /usr/include, saw a superlu folder, but no grep on tk or tcl. so tried $ sudo apt-get install tk-dev -seems to have gotten a lot of stuff - I don't know if that was necessary, or if you just needed ls -a, there is a tk and a tcl.8.4 folder with .h's in them

- ls -a | grep blt gives nothing $ sudo apt-get install blt-dev - now I get a grep blt!! and a blt.h, which is in the /usr/include - note: I think "-dev" stands for development

- Final Guess: TCL_INCLUDE = /usr/include/tcl8.4 TK_INCLUDE = /usr/include/tk BLT_INCLUDE = /usr/include 3.3.2010

- X11 $ xterm & ;# works so it looks like you already have X11

-Final Guess X_INCLUDE = /usr/X11 MASTER_INCLUDE = -I$(TCL_INCLUDE) -I$(TK_INCLUDE) -I$(BLT_INCLUDE) -Dlinux -DLINUX X_LIB = -L/usr/lib64/X11 -lX11

- SuperLU -Final Guess SUPERLUDIR = /usr/include/superlu SUPERLIB = /usr/lib64/libsuperlu.a

- UMFpack -couldn't find headers for UMFpack, so tried $ sudo apt-get install libsuitesparse-dev -give up and compile from source? http://linux.softpedia.com/progDownload/UMFPACK-Download-35440.html - dr. law has v5.0, so why bother to compile the "new" one, 5.2? $ cd $FLXSHOME/support/UMFPACKv5.0/UMFPACK - Edit the Makefile to select the system of your choice and then edit that file. $ gedit Makefile & - select "include Make.linux" - nothing to select!! just compile everything $ gedit Make.linux & -You'll need to again indicate the location of the BLAS lib, and you do not need to compile a version for matlab - dr. law's advice was not helpful: try the UMFPACK/README.txt

"GNUmakefile a nice Makefile, for GNU make" "Makefile an ugly Unix Makefile (for older make's)"

"To configure, edit the UFconfig/UFconfig.mk file (otherwise, you may get warnings that the BLAS (dgemm, etc) are not found). $ gedit UF/config/UFconfig.mk -To enable an option of the form "# OPTION = ...", edit this file and # delete the "#" in the first column of the option you wish to use. - uncommented the 64 bit stuff... $ cd to UMFPACK $ make - had some errors while compiling, first with xerbla, seems to be typo in the name of the library? -they suggest: # XERBLA = ../../UFconfig/xerbla/libxerbla.a -but in that directory is only libcerbla.a, so changed: XERBLA = ../../UFconfig/xerbla/libcerbla.a -typo? 3.4.2010 - had a second err about "can't find -lgoto64", which is in UFconfig.mk for blas 64 bit. I just commented it out... and it compiled. we'll see if it works with floods compile... but first:

$ make clean

-See the User Guide (Doc/UserGuide.pdf), or ../UFconfig/UFconfig.mk for more details (including options for compiling in 64-bit mode).

- see if the flooxs make will do the umf make as well, since the directories are there. - no, wait, then you won't have the right path for blas in umf :( make doesn't work anyway...

- Configure FLOOXS source file to use the arch file specified (make ARCH depend) $ cd $FLXSHOME/src #$ dependscript linux ;# the linux should be the system you are compiling for and match the arch file -dependscript not found - I think this is old... $ make ARCH=linux seqs $ make ARCH=linux depend

- Configure one more thing: create a library subdirectory for this architecture. Use: $ mkdir $FLXSHOME/lib/linux  ;#replace linux with the name of the architecture you have $ make ARCH=linux ;#in the src directory.

- This should do it. If you have compile errors or load errors, suspect the arch file that you created.

12. Compile Floops/Floods - make depend was ok - make had LOTS of errors :(:(

11. Do a CVS update (how to do this...) $ sudo apt-get install cvs - look in $FLXSHOME/src/CVS (contains 3 files) $ gedit Root -replace line there with: :ext:nrowsey@swamp2.tec.ufl.edu:/home/killebrew0/flooxs/cur/cvsroot $ cd $FLXSHOME/src $ cvs update -log into swamp2 with your passwd

-ok problem with flooxs make depend: Makefile:25: *** commands commence before first target. Stop.

-ok your version was not the same as Dr. Law's new version, and cvs did a merge: "Files with conflicts will have conflict markers in them. Conflict markers look like: <<<<<<< filename your lines ======= other person's lines >>>>>>> current version"

- The error above is telling me that I should look in the Makefile near line 25. I looked there, saw the conflict, then decided to delete my lines, and keep the "other person's" bc the other person is Dr. Law, but I'll make a backup first

$ cd $FLXSHOME/src $ cp Makefile Makefile_bk $ gedit Makefile &

- error in src/math dir near line 12, same kind so, $ cd math $ gedit Makefile & $ gedit blas.h & # conflict here too 3/5/2010 - seems dsp_defs.h is old, and slu_ddefs.h is new better one. Go through the files in the math directory and replace dsp_defs.h with slu_ddefs.h. Hopefully, that will do the trick. $ cd src/math $ grep -r "dsp_defs.h" . ./Superlu.h:#include "dsp_defs.h" $ gedit Superlu.h & - replace with #include "slu_ddefs.h"

- Where should SUPERLUDIR point? "It looks like it should point to the home directory of the install of SuperLU, so in your case it doesn't really work. I think you need to edit the Makefile in the math directory. There is an INCL definition that uses SUPERLUDIR. Change that to -I/usr/include/super..... - whatever your directory location.

- error: -I/home/nicrawfolerd/flooxs/rel2008/support/UMFPACKv5.0/AMD/Include Sles.cc Sles.cc: In member function ‘virtual int SlesMatrix::FinishLoad()’: Sles.cc:55: error: ‘MAT_ROWS_SORTED’ was not declared in this scope Sles.cc: In member function ‘virtual void SlesPrecond::NewMatrix(Matrix&)’: Sles.cc:111: error: ‘PCFactorSetMatOrdering’ was not declared in this scope make[1]: *** [/home/nicrawfolerd/flooxs/rel2008/lib/linux64/math.a(Sles.o)] Error 1 make[1]: Leaving directory `/home/nicrawfolerd/flooxs/rel2008/src/math' make: *** [libs] Error 1

"I'm not sure why, but I also know we don't use sles very often. Comment out the offending lines and let's see if we can get further."

so: line 55: // ierr = MatSetOption(mat, MAT_ROWS_SORTED); //comment out to help compile?

line 111: has comment below it: // ierr = PCFactorSetMatOrdering(pc, matord);

///// Newer versions of PETSC might work with this - great! I have a newer version of PETSC!! // ierr = PCFactorSetMatOrderingType(pc, matord); - this didn't work so I commented it out too


3/11/2010 - sles seems to be a problem. check SLESDIR in arch/linux64 file: - in old slesdir is: nicrawfolerd@bluebox:~/flooxs/rel2008/support/petsc-2.3.2-p7/lib/linux-gnu-c-debug$ ls libpetsc.a libpetscdm.a libpetscmat.a libpetscts.a libpetsccontrib.a libpetscksp.a libpetscsnes.a libpetscvec.a - new slesdir is?: nicrawfolerd@bluebox:~/flooxs/rel2008/support/petsc-3.0.0-p11/linux-gnu-amd64/lib$ ls libfblas.a libmpich.a libpetsc.a libpetscmat.a libprometheus.a libflapack.a libmpichcxx.a libpetsccontrib.a libpetscsnes.a libpromfei.a libfmpich.a libmpichf90.a libpetscdm.a libpetscts.a pkgconfig libmetis.a libparmetis.a libpetscksp.a libpetscvec.a - seems to have all the same files and more - see email to dr. law - MPILIB has: -old: nicrawfolerd@bluebox:~/flooxs/rel2008/support/petsc-2.3.2-p7/externalpackages/mpich2-1.0.4p1/lib$ ls libfmpich.a libmpich.a libmpichcxx.a libmpichf90.a pkglist st2m5gyL -new: nicrawfolerd@bluebox:~/flooxs/rel2008/support/petsc-3.0.0-p11/externalpackages/mpich2-1.0.8/lib$ ls pkglist

- ew - not the same except for package list... - changed paths for MPILIB and MPIDIR (see arch/linux64 file) -same error - tried to recompile petsc without prometheus and metis (edit linux-gnu-amd64.py, etc) - ok, this got rid of the prometheus and metis erros, but still have 2 errors: /home/nicrawfolerd/flooxs/rel2008/support/petsc-3.0.0-p11/linux-gnu-amd64/lib/libpetscdm.a(ao.o): In function `AOApplicationToPetscIS': ao.c:(.text+0x296): undefined reference to `ISStrideToGeneral'

/home/nicrawfolerd/flooxs/rel2008/support/petsc-3.0.0-p11/linux-gnu-amd64/lib/libpetscdm.a(ao.o): In function `AOPetscToApplicationIS': ao.c:(.text+0x467): undefined reference to `ISStrideToGeneral' collect2: ld returned 1 exit status Command exited with non-zero status 1

- seems to be a problem with libpetscdm.a(ao.o) whatever ao.o means - I looke in this file, commented out all lines with "ISStrideToGeneral" - floods compiled - I can run my files, but the graphing is broken

- fix BLT??




- this superlu stuff is ridiculous. try installing the flooxs/support version:

#$ sudo apt-get install linux-kernel-headers

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