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2. Navigate to the Windows Store. Search for Ubuntu and install the program
2. Navigate to the Windows Store. Search for Ubuntu and install the program


3.  
If you've never used Linux / Unix before, you might find the following flooxs installation instructions confusing. I've started a page to explain some [[basic unix concepts]] that held me up as I was learning and trying to install flooxs.
 
= Install Xming on Windows =


If you've never used Linux / Unix before, you might find the following flooxs installation instructions confusing. I've started a page to explain some [[basic unix concepts]] that held me up as I was learning and trying to install flooxs.
Navigate to https://sourceforge.net/projects/xming/ in a browser on Windows.  Download Xming and install it. This program must either be run before using graphics in Bash/Ubuntu or placed in your startup programs.


= Get Your Flooxs! =
= Get Your Flooxs! =
== From Download ==
1. Download the software and put it on your hard drive in a directory called flooxs
1. Download the software and put it on your hard drive in a directory called flooxs
         $ mkdir ~/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)
         - go to [[Download]]
, download the latest linux executable file (get the one that says linux)


2. Unpack the flooxs file
2. Unpack the flooxs file
        Double click -> Export
This should make a directory called rel2008. Put it in your new Flooxs folder by copying it from its location in Windows to Bash/Ubuntu:  
This should make a directory called rel2008. Put it in your new flooxs folder. Inside rel2008 you should have these folders:
        $ cd ~/flooxs/rel2008
        $ ls
        arch  bin  help  lib  Params  src  support  TclLib  Test


To install flooxs, we first must install several supporting programs (such as math or graphing packages) in the support directory. Then, we will go into the src (short for "source") directory and compile flooxs from there.
        $ cp /mnt/c/Users/[Windows Username]/[File Location] [Location you want Flooxs in Bash/Ubuntu]


= Get PETSC math package, with BLAS, LAPACK and MPI =
== From Git ==
In this section, we will download, configure, and compile three supporting math packages that flooxs uses to solve matrix problems, as well as a compiler that these math packages use.
Clone the Git repository. You need to have git permissions from Mark Law
        $ git clone https://github.com/marklaw59/flooxs.git


= Edit FLOOXS Library Paths in your Arch File =
= Edit FLOOXS Library Paths in your Arch File =
In this section, we will edit a long list of library paths contained in your arch file. These paths tell flooxs where you have installed all the packages from above. First, let's find the file with all these paths:
You should have no issues with libraries if you use the linux arch file provided to you ([[linux]]). However, if you do have issues with libraries then you must locate the directories of the libraries and put the paths into the $FLXSHOME/arch/Linux file.
        $ cd $FLXSHOME/arch
 
        $ cp linux64 linux64_bk ;# (makes a backup)
= Compile Flooxs =
         $ gedit linux64 &
== Install Public Domain Libraries used in the compilation ==
This part is painstakingly annoying. For *each* path in this file, I had to navigate to that directory in an old, working flooxs directory, find what files were there, and then use
3. Open the Bash/Ubuntu terminal that you just installed. Run the following commands (They may require a system restart between them):
         $ find . -name "*file*" -print
        sudo do-release-upgrade -p
to see where the new ones were. Most of the time you are looking for .h or .a files, which are [http://en.wikipedia.org/wiki/Header_file headers] and [http://en.wikipedia.org/wiki/Library_%28computing%29 library files] respectively.
         sudo apt update && sudo apt upgrade
         sudo apt install tk tk-dev tcl tcl-dev libsuitesparse-dev libplplot-dev plplot-tcl plplot-driver-cairo libopenblas-dev
 
== Set the required environment variable ==
4. Open your ~/.bashrc or create a FLOOXS environment variable script. Add or make sure the following lines are in the file:
        export DISPLAY=localhost:0
        export FLXSHOME=/home/[Your Flooxs Folder Location]
        export PL_LIBRARY=/usr/share/plplot5.13.0/tcl/
Note: the plplot variable depends on the plplot version can vary by linux distribution.  


Here is my completed arch file that resulted in a successful compile and future operation of flooxs: [[linux64]]. You can see I commented out the old paths with #, and put my new paths underneath.
5. If you choose a environment variable script, make sure to source the file before using FLOOXS.


= Compile Flooxs =
== Compile ==
If you get warnings, probably this is okay. Errors will never be okay. In general, you should resolve any errors in the "make depend" before trying to make. When you get an error, scroll up to see what directory you were in, check and see what file the error is in, and what line number it is giving you. Most likely if you get errors you simply did not set your paths correctly in your arch file.
If you get warnings, probably this is okay. Errors will never be okay. In general, you should resolve any errors in the "make depend" before trying to make. When you get an error, scroll up to see what directory you were in, check and see what file the error is in, and what line number it is giving you. Most likely if you get errors you simply did not set your paths correctly in your arch file.
Compile with cmake (prefered):
        $ cd $FLXSHOME
        $ mkdir release && cd release
        $ cmake ..
        $ make -j8
        $ sudo make install
Or with make:
         $ cd $FLXSHOME/src
         $ cd $FLXSHOME/src
         $ make depend ARCH=linux
         $ make new ARCH=linux
        $ make ARCH=linux


= Do a CVS update if you want =
= Do a CVS update if you want =
If you are one of Dr. Law's students and you have a login to our computers, you can do a [http://en.wikipedia.org/wiki/Concurrent_Versions_System CVS update] to get the latest version of the flooxs code. Don't worry if you cannot do this. The 2008 version works fine.
If you are one of Dr. Law's students and you have a login to our computers, you can do a [http://en.wikipedia.org/wiki/Concurrent_Versions_System CVS update] to get the latest version of the flooxs code.


First, get cvs (concurrent versioning system) for your Ubuntu:
First, get cvs (concurrent versioning system) for your Ubuntu:
         $ sudo apt-get install cvs
         $ sudo apt-get install cvs
         $ cd $FLXSHOME/src/CVS (contains 3 files)
         $ [[setcvsuname.sh]] [Your Login]
        $ ls
        $ gedit Root
Replace line there with:
        :ext:<username>@swamp2.tec.ufl.edu:/home/killebrew0/flooxs/cur/cvsroot
where <username> is YOUR username. You will have to do this in each of the subdirectories too. Each subdirectory has a CVS directory with Root in it. You can use recursive [http://en.wikipedia.org/wiki/Grep grep] to find these directories:
        $ cd $FLXSHOME/src
        $ grep -r swamp2 .
This last command uses the grep program (grep) to recursively search (-r) for the pattern (swamp2) in the directory you are in (.) which because of the previous line is ($FLXSHOME/src). You will have to fix the "Root" file in each of the directories that this command prints out to have your username. You can "man grep" to find other options that will print prettier output, and you can also write your own script that will go in and replace your username automatically. Go ahead and post here if you make a script.


When you're done with that, then you can do the CVS update:
When you're done with that, then you can do the CVS update:
         $ cd $FLXSHOME/src
         $ cd $FLXSHOME/src
         $ cvs update
         $ cvs update
         -log into swamp2 with your passwd
         -log in with your passwd


If you do a cvs update, there may be some [http://www.google.com/search?hl=en&client=firefox-a&hs=s8f&rls=com.ubuntu%3Aen-US%3Aofficial&q=resolve+cvs+conflict&aq=f&aqi=g-l1&aql=&oq=&gs_rfai= conflicts] with the new version that the cvs program was not intelligent enough to know how to merge. This is normal. As the intelligent user, you must resolve these conflicts. But how, you ask? Files with conflicts will have conflict markers in them. Conflict markers look like:
If you do a cvs update, there may be some [http://www.google.com/search?hl=en&client=firefox-a&hs=s8f&rls=com.ubuntu%3Aen-US%3Aofficial&q=resolve+cvs+conflict&aq=f&aqi=g-l1&aql=&oq=&gs_rfai= conflicts] with the new version that the cvs program was not intelligent enough to know how to merge. This is normal. As the intelligent user, you must resolve these conflicts. But how, you ask? Files with conflicts will have conflict markers in them. Conflict markers look like:
Line 83: Line 93:
         $ gedit blas.h & # conflict here too
         $ gedit blas.h & # conflict here too


= some other errors I got and how I resolved them =
= Common Issues =
guess: 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" .
'''1)''' The plotting utility is not working. Here you most likely did not start Xming or you did not add "export DISPLAY=localhost:0" to your ~/.bashrc
                ./Superlu.h:#include "dsp_defs.h"
 
        $ gedit Superlu.h &
'''2)''' Some file names have case issues. Generally fixed with:
- replace with #include "slu_ddefs.h"
    mv LevelSet/LayerGRid.cc LevelSet/LayerGrid.cc
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.
    mv diffuse/newton.cc diffuse/Newton.cc
        - error:
 
        -I/home/nicrawfolerd/flooxs/rel2008/support/UMFPACKv5.0/AMD/Include Sles.cc
'''3)''' Some files might need a string.h include. The most common file where this is necessary is src/BasePDE/ErrInfo.h
        Sles.cc: In member function ‘virtual int SlesMatrix::FinishLoad()’:
    #include <string.h>     //to the top of src/BasePDE/ErrInfo.h
        Sles.cc:55: error: ‘MAT_ROWS_SORTED’ was not declared in this scope
 
        Sles.cc: In member function ‘virtual void SlesPrecond::NewMatrix(Matrix&)’:
'''4)''' Makefile.linux.depend doesn't exist. Execute the following:
        Sles.cc:111: error: ‘PCFactorSetMatOrdering’ was not declared in this scope
    touch Makefile.linux.depend
        make[1]: *** [/home/nicrawfolerd/flooxs/rel2008/lib/linux64/math.a(Sles.o)] Error 1
    find . -type d -exec touch Makefile.linux.depend \;
        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);
but this didn't work so I commented that last one out too.
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
        - 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
These are not the same except for package list. I changed paths for MPILIB and MPIDIR (see arch/linux64 file), but got the same error. Finally, I recompiled petsc without prometheus and metis (edit linux-gnu-amd64.py, etc), and 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


This seems to be a problem with libpetscdm.a(ao.o). So, I looked in this file (ao.o) and commented out all lines with "ISStrideToGeneral". Flooxs compiled with no errors. However, the graphing was broken... turns out there's some issues with ./bltwish on newer blt versions. I solved this by downgrading my tcl/tk to v8.3, and updated the tcl/tk/blt sections in this wiki to reflect that change on 1/1/2010.
'''5)''' For older versions of flooxs, $(MASTER_INCLUDE) is not present in all makefiles.

Latest revision as of 17:00, 9 August 2023

Today is 9/11/2018 - These are notes on how to install instructions for flooxs on 64-bit Ubuntu 18.04 Subsystem for Windows. These instructions are intended for linux/unix beginners.

Get Linux Subsystem for Windows - and check out basic concepts page

First, install the Linux Subsystem for Windows to enable the platform. If you already have Ubuntu installed, skip to step 3.

1. Open the Windows PowerShell as an administrator and run the following command: 

       Enable-WindowsOptionalFeature -Online -FeatureName Microsoft-Windows-Subsystem-Linux

2. Navigate to the Windows Store. Search for Ubuntu and install the program

If you've never used Linux / Unix before, you might find the following flooxs installation instructions confusing. I've started a page to explain some basic unix concepts that held me up as I was learning and trying to install flooxs.

Install Xming on Windows

Navigate to https://sourceforge.net/projects/xming/ in a browser on Windows. Download Xming and install it. This program must either be run before using graphics in Bash/Ubuntu or placed in your startup programs.

Get Your Flooxs!

From Download

1. Download the software and put it on your hard drive in a directory called flooxs 

       $ mkdir ~/flooxs
       - go to Download

, download the latest linux executable file (get the one that says linux)

2. Unpack the flooxs file This should make a directory called rel2008. Put it in your new Flooxs folder by copying it from its location in Windows to Bash/Ubuntu: 

       $ cp /mnt/c/Users/[Windows Username]/[File Location] [Location you want Flooxs in Bash/Ubuntu]

From Git

Clone the Git repository. You need to have git permissions from Mark Law 

       $ git clone https://github.com/marklaw59/flooxs.git

Edit FLOOXS Library Paths in your Arch File

You should have no issues with libraries if you use the linux arch file provided to you (linux). However, if you do have issues with libraries then you must locate the directories of the libraries and put the paths into the $FLXSHOME/arch/Linux file.

Compile Flooxs

Install Public Domain Libraries used in the compilation

3. Open the Bash/Ubuntu terminal that you just installed. Run the following commands (They may require a system restart between them): 

       sudo do-release-upgrade -p
       sudo apt update && sudo apt upgrade
       sudo apt install tk tk-dev tcl tcl-dev libsuitesparse-dev libplplot-dev plplot-tcl plplot-driver-cairo libopenblas-dev

Set the required environment variable

4. Open your ~/.bashrc or create a FLOOXS environment variable script. Add or make sure the following lines are in the file: 

       export DISPLAY=localhost:0
       export FLXSHOME=/home/[Your Flooxs Folder Location]
       export PL_LIBRARY=/usr/share/plplot5.13.0/tcl/

Note: the plplot variable depends on the plplot version can vary by linux distribution.

5. If you choose a environment variable script, make sure to source the file before using FLOOXS.

Compile

If you get warnings, probably this is okay. Errors will never be okay. In general, you should resolve any errors in the "make depend" before trying to make. When you get an error, scroll up to see what directory you were in, check and see what file the error is in, and what line number it is giving you. Most likely if you get errors you simply did not set your paths correctly in your arch file.

Compile with cmake (prefered): 

       $ cd $FLXSHOME
       $ mkdir release && cd release
       $ cmake .. 
       $ make -j8
       $ sudo make install


Or with make: 

       $ cd $FLXSHOME/src
       $ make new ARCH=linux

Do a CVS update if you want

If you are one of Dr. Law's students and you have a login to our computers, you can do a CVS update to get the latest version of the flooxs code.

First, get cvs (concurrent versioning system) for your Ubuntu: 

       $ sudo apt-get install cvs
       $ setcvsuname.sh [Your Login]

When you're done with that, then you can do the CVS update: 

       $ cd $FLXSHOME/src
       $ cvs update
       -log in with your passwd

If you do a cvs update, there may be some conflicts with the new version that the cvs program was not intelligent enough to know how to merge. This is normal. As the intelligent user, you must resolve these conflicts. But how, you ask? Files with conflicts will have conflict markers in them. Conflict markers look like: 

               <<<<<<< filename
               your lines
               =======
               other person's lines
               >>>>>> current version"

In this case, you want the other person's line, as this is Dr. Law's new version, and not your old version. Of course, you can always make a backup first. For example, I used this method to find the conflicts, then fixed them by hand: 

       $ find $FLXSHOME -name "<<<<<" -print
       $ cd $FLXSHOME/src
       $ cp Makefile Makefile_bk
       $ gedit Makefile &

       $ cd math
       $ gedit Makefile &
       $ gedit blas.h & # conflict here too

Common Issues

1) The plotting utility is not working. Here you most likely did not start Xming or you did not add "export DISPLAY=localhost:0" to your ~/.bashrc

2) Some file names have case issues. Generally fixed with: 

   mv LevelSet/LayerGRid.cc LevelSet/LayerGrid.cc
   mv diffuse/newton.cc diffuse/Newton.cc

3) Some files might need a string.h include. The most common file where this is necessary is src/BasePDE/ErrInfo.h 

   #include <string.h>     //to the top of src/BasePDE/ErrInfo.h

4) Makefile.linux.depend doesn't exist. Execute the following: 

   touch Makefile.linux.depend
   find . -type d -exec touch Makefile.linux.depend \;

5) For older versions of flooxs, $(MASTER_INCLUDE) is not present in all makefiles.

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