PHASTA Wiki - User contributions [en]

Main Page

2020-09-02T21:55:04Z

Matthb2:

Welcome to the Wiki for the [https://github.com/phasta/phasta PHASTA] project at the University of Colorado, Boulder. The information contained within is mostly systems documentation and usage information for software which may or may not be public yet, but feel free to look around.

[[Special:AllPages|List Of All Pages]]

[[Tutorial Video Overviews]]

[[:Category:Software|Available Software]]

[[:Category:Software Engineering|Software Engineering]]

[[UNIX|Getting Started with UNIX]]

[[:Category:Post-processing|Post-processing and Visualization]]

[[Making_A_New_Wiki|Making A New Wiki Page]]

[[:Special:Categories]]

TotalView

2014-05-02T22:47:18Z

Matthb2:

We currently have an evaluation license of the TotalView graphical/parallel debugger. Please give it a try and let Ben know if you have any problems

==Running==
soft add +totalview-8.13.0
mpirun -tv -np 1 your_program

==ReplayEngine/Reverse Debugging==

mpirun -mca mpool_rdma_rcache_size_limit 1 -x IBV_FORK_SAFE=1 -x LD_PRELOAD=/usr/local/toolworks/totalview.8.13.0-0/linux-x86-64/lib/undodb_infiniband_preload_x64.so -tv -np 1 your_program

(see the TotalView user's guide for more information)

==Documentation==
http://www.roguewave.com/support/product-documentation/totalview.aspx

2013-07-15T20:06:34Z

Matthb2:

[[Category:Software]]

Matlab is installed only on Viz001 and Viz002 (since we only have node-locked licenses). Several recent versions are installed in /opt/MATLAB. Currently, the full path to the latest version is:

/opt/matlab/R2013a/bin/matlab

The licenses expire periodically, but can be renewed. If you need an older version and find that the license has expired, please email Benjamin.A.Matthews@Colorado.edu

Address Sanitizer

2013-07-15T19:59:47Z

Matthb2:

Address Sanitizer

2013-07-15T19:59:00Z

Matthb2: Created page with "== Introduction == Address sanitizer is a compiler extension and runtime library used for debugging memory errors. It works by introducing extra "canary" regions around memory al..."

== Introduction ==
Address sanitizer is a compiler extension and runtime library used for debugging memory errors. It works by introducing extra "canary" regions around memory allocated by your program, and checks for accesses to those regions. This allows it to detect when your program accesses memory that has not been properly allocated. You can read more about how address sanitizer works [[https://code.google.com/p/address-sanitizer/wiki/AddressSanitizerAlgorithm here]]

== Use ==
Address sanitizer is available in newer versions of GCC (>= 4.8.0) and Clang (>=3.0?). On the Viz nodes, you'll want to use GCC.

First, load GCC 4.8

soft add +gcc-4.8.1

Then compile your code using appropriate flags. If you're using CMake, you'll want to set the CMAKE_C_FLAGS, CMAKE_CXX_FLAGS and CMAKE_Fortran_FLAGS variables (these are "advanced" - you'll need to press the "t" key in ccmake to see them)

gcc -fsanitize=address -O0 -fno-omit-frame-pointer -g test.c

Next run your program normally. If it runs to completion, congratulations, it's likely you don't have any bad accesses. Otherwise, your program will crash and print a couple pages of information. You can use this output to find the problem (the "addr2line" command may be helpful). An easier way is to use gdb:

In serial:
gdb my_program
break __asan_report_error
run

At which point, your program should stop and return you to a gdb prompt right after the bad access occurs. you can use the
bt
command to see where the code stopped and debug as you normally would with gdb.

In parallel, the procedure is basically the same, but you'll need to use multiple copies of gdb (or a parallel debugger if you're using a system on which one is available). See the [[Debugging]] page for more information on using gdb in parallel.

Adding CMAKE To PHASTA

2013-07-02T03:45:10Z

Matthb2:

If you'd like to use the new CMake based build system as described on the [[Compiling PHASTA With CMake]] page, but haven't merged your copy with [[https://redmine.scorec.rpi.edu/anonsvn/phasta SVN trunk]] recently, you can follow these steps to add CMake support to your fork.

First, download the CMake build scripts:

git clone https://github.com/matthb2/phasta-buildsystem.git

Next, we'll re-arrange your checkout of PHASTA to remove any redundant directories

cd phasta
mv phSolver tmp
mv tmp/phSolver ./
rmdir tmp
#and so on with each directory that you have

Once that's done, you'll need to copy all the CMakeLists.txt files into their respective directories:
#starting from your phasta source directory:
for i in `find ../phasta-buildsystem -name 'CMakeLists.txt' | sed 's:\.\.\/::g' | sed 's:CMakeLists.txt$::g' | sed 's:^phasta\-buildsystem\/::g'`; do cp ../phasta-buildsystem/$i/CMakeLists.txt ./$i/

From this point, if you're on a fairly normal system, you can probably just build using CMake. That said, if you want your setup to be robust, it's a good idea to make some minor code changes in order to allow CMake to compute the necessary name mangling for the Fortran callable C functions.

CMake will generate a header file called "FCMangle.h" which supplies some macros. The one we're interested in is called
FortranCInterface_GLOBAL_()
This macro takes two arguments, both of which are the name of the global symbol that should be Fortran callable. The first argument should be all lowercase, and the second should be all uppercase. The macro returns the Fortran name of the symbol.

For example, if I have a C function "foo()" that I want to call from Fortran, in my C header, I'd add these lines:
#include <FCMangle.h>
#define foo FortranCInterface_GLOBAL_(foo,FOO)

To take advantage of this in PHASTA, you'll find blocks of code that look like:

#ifdef ibm
#define something
#endif
#ifdef aix
#define something
#endif

Which should be replaced by calls to FortranCInterface_GLOBAL_. I've found that grepping for "ibm" catches most of these. If you fail to update any of these pieces of code, you'll see linker errors on certain platforms.

Note that to avoid another second class of bug, we've also been removing the trailing underscores from any functions that have them. For example "readheader_()" becomes "readheader()"

There is a (slightly outdated) video showing this process on an arbitrary fork of PHASTA available [[http://fluid.colorado.edu/~matthb2/videos/phastatocmake/ here]]

If you have any problems with this process, feel free to email [[mailto:Benjamin.A.MatthewsATcolorado.edu Ben]] and please share any lessons learned on this page.

Adding CMAKE To PHASTA

2013-07-02T03:44:08Z

Matthb2: Created page with "If you'd like to use the new CMake based build system as described on the Compiling PHASTA With CMake page, but haven't merged your copy with [[https://redmine.scorec.rpi.edu..."

If you'd like to use the new CMake based build system as described on the [[Compiling PHASTA With CMake]] page, but haven't merged your copy with [[https://redmine.scorec.rpi.edu/anonsvn/phasta SVN trunk]] recently, you can follow these steps to add CMake support to your fork.

First, download the CMake build scripts:

git clone https://github.com/matthb2/phasta-buildsystem.git

Next, we'll re-arrange your checkout of PHASTA to remove any redundant directories

cd phasta
mv phSolver tmp
mv tmp/phSolver ./
rmdir tmp
#and so on with each directory that you have

Once that's done, you'll need to copy all the CMakeLists.txt files into their respective directories:
#starting from your phasta source directory:
for i in `find ../phasta-buildsystem -name 'CMakeLists.txt' | sed 's:\.\.\/::g' | sed 's:CMakeLists.txt$::g' | sed 's:^phasta\-buildsystem\/::g'`; do cp ../phasta-buildsystem/$i/CMakeLists.txt ./$i/

From this point, if you're on a fairly normal system, you can probably just build using CMake. That said, if you want your setup to be robust, it's a good idea to make some minor code changes in order to allow CMake to compute the necessary name mangling for the Fortran callable C functions.

CMake will generate a header file called "FCMangle.h" which supplies some macros. The one we're interested in is called
FortranCInterface_GLOBAL_()
This macro takes two arguments, both of which are the name of the global symbol that should be Fortran callable. The first argument should be all lowercase, and the second should be all uppercase. The macro returns the Fortran name of the symbol.

For example, if I have a C function "foo()" that I want to call from Fortran, in my C header, I'd add these lines:
#include <FCMangle.h>
#define foo FortranCInterface_GLOBAL_(foo,FOO)

To take advantage of this in PHASTA, you'll find blocks of code that look like:

#ifdef ibm
#define something
#endif
#ifdef aix
#define something
#endif

Which should be replaced by calls to FortranCInterface_GLOBAL_. I've found that grepping for "ibm" catches most of these. If you fail to update any of these pieces of code, you'll see linker errors on certain platforms.

Note that to avoid another second class of bug, we've also been removing the trailing underscores from any functions that have them. For example "readheader_()" becomes "readheader()"

There is a (slightly outdated) video showing this process on an arbitrary fork of PHASTA available [[http://fluid.colorado.edu/~matthb2/videos/phastatocmake/ here]]

If you have any problems with this process, feel free to email [[mailto:Benjamin.A.Matthews AT colorado.edu Ben]] and please share any lessons learned on this page.

PHASTA/Compiling PHASTA With CMake

2013-07-02T03:02:15Z

Matthb2: /* Cross Compiling on IBM's BlueGene/Q */

There is an unofficial, but popular version of the PHASTA solver which uses a [[http://cmake.org CMake]] based build system. Generally, an out-of-source build is used, meaning that you have a separate directory for your executables and intermediate files.

Assuming you have your desired compiler and a current version of CMake (2.8.5 or newer) in your path, you must first create and change into an empty directory to store your build

mkdir build
cd build

You can then run cmake to create your makefile

If you're using the Intel compiler suite:

CC=icc CXX=icpc FC=ifort ccmake ../phasta

If you're using the PGI compiler suite:

CC=pgcc CXX=pgCC FC=pgfortran ccmake ../phasta

If you're using the GNU toolchain:

CC=gcc CXX=g++ FC=gfortran ccmake ../phasta

This will open a "GUI" of sorts. You can use the arrow keys to navigate. Press enter to edit the highlighted field, and then enter again to save your change. Press the "c" key to compute the options. Press "g" to write out the makefile and quit. You'll need to press "c" several times, and fill in any desired options before you can generate your makefile.

You may want to set the "CMAKE_BUILD_TYPE" field to either "Release" or "Debug" to get an optimized build or a debugable build respectively.

Once you've completed this process, you can simply run "make" to build the code. The executable will be in the "bin" sub-directory of your build directory.
make

== Tips ==

on the viz nodes, run "soft add +cmake" to get an appropriate version of CMake.

on Janus, run "module load cmake" to get an appropriate version of CMake

If you run into trouble, it may be useful to see how the compiler is being invoked. You can do this by running:

make VERBOSE=1

(after having already run cmake)

To add additional compiler flags, use the CMAKE_C_FLAGS, CMAKE_CXX_FLAGS and CMAKE_Fortran_FLAGS fields when you configure

The build options are in a (somewhat) human readable format in a file called "CMakeCache.txt" in the root of your build directory - this can be very useful if you need to figure out which options were used for a particular build.

If you add a new file, you need to tell CMake that the source has changed (this is not usually necessary if you've simply edited an existing source file). You can do this as follows (from your build directory):
touch CMakeCache.txt

CMake uses the MPI wrappers to find your MPI install by default - mpicc and mpif90 must be in your PATH prior to running ccmake

If you'd like to use CMake in a non-interactive fashion, you can use "cmake" instead of "ccmake" and specify and options on the command line by prepending them with "-D". For example:

cmake -DCMAKE_BUILD_TYPE=Release -DPHASTA_INCOMPRESSIBLE=ON -DACUSOLVE_LIB=$HOME/libles.a ../phasta
make

The incompressible solver is disabled by default. You'll need to set the PHASTA_INCOMPRESSIBLE option to "ON" and specify the full path to the Acusolve library when prompted.

A fairly generic version of PHASTA, which includes this build system, can be found on the viz nodes in /users/matthb2/phasta-tocmake/phasta

CMake supports generating scripts for other build tools, for example Xcode, Eclipse and Ninja. See the "cmake" manpage for more information.

Some compilers which can perform inter-procedural analysis have a hard time with PHASTA. See the [[Compilers]] page for information on disabling this optimization if linking takes too long

== Cross Compiling with CMake ==

CMake can cross compile PHASTA, for example on a BlueGene or Cray system. To do this, you simply need to provide an appropriate toolchain file specifying the path to the cross compilers and then build as normal.

ccmake -DCMAKE_TOOLCHAIN_FILE=some_file.cmake ../phasta

There are some toolchain files for systems that we commonly use available [[https://github.com/matthb2/CMakeToolchainFiles here]] (note that the BlueGene/Q toolchain files provided here expect a [[https://github.com/matthb2/CMake/tree/bgq patched version]] of CMake -- see below)

Kitware has some documentation on cross compiling with CMake [[http://www.cmake.org/Wiki/CMake_Cross_Compiling here]].

== Cross Compiling on IBM's BlueGene/Q ==

Currently, CMake doesn't officially have explicit support for BlueGene/Q (BlueGene/P is supported). While you should be able to use a toolchain file expecting one of the generic system types, we've modified the BG/P platform files for /Q, based on the setup used on [[http://alcf.anl.gov ALCF's]] systems (should work with most /Q systems). To use them, you need to add two files [[https://raw.github.com/matthb2/CMake/bgq/Modules/Platform/BlueGeneQ-base.cmake 1]] [[https://raw.github.com/matthb2/CMake/bgq/Modules/Platform/BlueGeneQ-static.cmake 2]] to your CMake install. For a normal install, these files should be placed in $prefix/share/cmake-2.8/Modules/Platform/

If you prefer, you can just directly install the "bgq" branch of [[https://github.com/matthb2/CMake/tree/bgq this repository]]

git clone https://github.com/matthb2/CMake.git
git checkout -b bgq origin/bgq
cd CMake
./configure --prefix=/some/path
make
make install
export PATH=/some/path:$PATH

You can then proceed as above, using [[https://raw.github.com/matthb2/CMakeToolchainFiles/master/BlueGene/Q/BGQ-XLMPI-toolchain.cmake this toolchain file]

Currently, the system software is changing very quickly. If you need a build of the proprietary library used for PHASTA's incompressible solver, please ask Ben or Michel (and tell them which Bluegene driver version you have)

== With gprof ==

(gnu compilers)

CC=gcc CXX=g++ FC=gfortran ccmake -DCMAKE_BUILD_TYPE=Debug -DCMAKE_C_FLAGS="-pg" -DCMAKE_CXX_FLAGS="-pg" -DCMAKE_Fortran_FLAGS="-pg" ../phasta

PHASTA/Compiling PHASTA With CMake

2012-11-08T05:10:02Z

Matthb2:

[[Category:Software]]

==NX==

UGS/Siemens NX 8.0 CAD/CAE package is available in /usr/local on the Linux machines and on the Windows workstations

You can launch it from portal0 as follows:

vglconnect -s viz001 #or one of the other graphics machiens
/usr/local/nx/ugs080/run.sh

You can launch the documentation by opening
/usr/local/nx/ugs080/ugdoc/html_files/nx_help/index.html in your favorite web browser. It is known to display correctly in Iceweasel but not the current version of Google Chrome

iceweasel file:///usr/local/nx/ugs080/ugdoc/html_files/nx_help/index.html

Installers are also available for personal machines. Please email Ben and/or Ken for instructions.

==Windows Troubleshooting==
If you get an error about License Bundles on the Windows machines, you need to open the NX "License Options" from the programs menu and select the current license bundles (if you follow the directions in the error message the settings won't persist). Feel free to follow along with this [[http://fluid.colorado.edu/~matthb2/videos/nx_license/nx_license_bundle.mp4 video]] (note that the available bundles may change over time, just choose the two that you're offered).

== CAST ==

The NX CAST tutorial library for version 8.0 is also installed. You can launch it in Iceweasel as with the main documentation:

iceweasel file:///usr/local/nx/cast080/html/index.html

== NASTRAN ==
NASTRAN is available on the Windows desktop in the lab. If you need it somewhere else, email Ben

UNIX

2012-11-01T21:49:44Z

Matthb2:

VNC

2012-11-01T18:01:44Z

Matthb2: /* Finding an Existing Session */

VNC is a tool which projects a GUI session over the network. If may be useful if you want to use GUI tools remotely when X forwarding performs poorly.

'''Warning: This is still being tested and should NOT be considered stable (portal0 may be rebooted without warning)'''
'''Warning: The vnc password is transmitted in clear text over the network and should not be considered secure'''

Portal0 is designated to host VNC sessions.

You can start a session as follows:

ssh jumpgate-phasta.colorado.edu
ssh portal0
source /etc/profile
start_vnc.sh

And follow the directions

(You may want to remember your password and port number so that you can reuse your session)

When you are done, end your session by
source /etc/profile
stop_vnc.sh

== OpenGL ==

Portal0 is equipped with a VirtualGL install which will allow you to use OpenGL programs (which do not use pthreads)

Simply wrap your OpenGL program with the "vglrun" command
vlgrun glxgears

If you have access to another VirtualGL server you can connect to it first (Portal0 doesn't have a particularly fast graphics processor)
vglconnect server
vglrun glxgears

Note that VGL uses a number of threads. If you have trouble with vglrun crashing with a message about Thread::Start() make sure you haven't set your stack size too large (remove any ulimit -s or ulimit -n calls from your shell start scripts)

== Clients ==

Portal0 uses TurboVNC from the VirtualGL project, available from http://www.virtualgl.org/Downloads/TurboVNC

Other VNC viewers will also work, such as TightVNC and RealVNC

== View Only Mode ==

To share your desktop with another user in view only mode set a view only password
by running
vncpasswd

Have the other user connect in the same way you would but have them set their viewer to be in view only mode and use your view only password. Typically this is done as follows:
vncviewer -viewonly

== Windows ==
The PuTTY SSH client can handle ssh tunneling on Windows based machines. You can download it here: http://www.chiark.greenend.org.uk/~sgtatham/putty/

When you open putty, enter jumpgate-phasta.colorado.edu as in the Host Name box. Then click the + button next to SSH on the left pane (to expand the SSH tree node). Choose the Tunnels page. The start_vnc.sh script should tell you to run "ssh -L????:portal0:???? jumpgate-phasta.colorado.edu" on your machine. Enter the number between the -L and the first colon in the "Source port" box. Enter the rest in the Destination box (starting with portal0) and '''click the add button'''. Then click "Open" and login as normal. You will then be able to use a vncviewer as instructed by the script.

Example:

The script says:
ssh -L5905:portal0:5900 jumpgate-phasta.colorado.edu
enter 5905 in the Source port box
enter portal0:5900 in the destination box.

Try using this viewer utility
http://www.tightvnc.com/download/1.3.10/tightvnc-1.3.10_x86_viewer.zip

== Web Based Viewer ==

If you can't or don't want to install a VNC viewer you can use a Java based one. You will need a JVM and a Java browser plugin. You will also need the port that the start_vnc script assigned you to be free on your local computer

Forward your session through jumpgate as before before, adding a second port, 580n. For example, if the script tells you to

ssh -L5905:portal0:5902 jumpgate-phasta.colorado.edu you should
ssh -L5902:portal0:5902 -L5802:portal0:5802 jumpgate-phasta.colorado.edu
Then point your browser to http://localhost:5802 and log in with the password specified by the script when prompted. (Replace 2 with the value specified by the script)

== Changing the Size (Resolution) of an Existing Session ==

You can usually use the "xrandr" tool to change the resolution of a running vnc session. First you'll need to know your session's display number (this should be the last digit or two of the port number). For example, if your VNC session is running on port 5902, then your screen number should be :2. For this example, we'll use screen 2.

Once you know your screen number, you can see the list of supported modes as follows:
xrandr -display :2

Once you pick the one you want (generally the same size or smaller than the native resolution of your client), you can choose it by running a command like
xrandr -s 1400x1050 -display :2

(this example will set the resolution to 1400 pixels by 1050 pixels)

You'll probably be disconnected at this point, but when you reconnect your screen size should be changed (hopefully without crashing your running programs).

== Finding an Existing Session ==
SSH to portal0 and then run:
/opt/vnc_script/findsession.sh

Which will return the shortened port number of each of your currently running sessions.

== Troubleshooting ==

If you have used vncserver (It doesn't matter which version) on a SCOREC machine before, you will need to clear your vnc settings for the script to work. You can do this by running rm -rf ~/.vnc

stop_vnc.sh may display some errors; this is normal.

If you have trouble deleting ~/.vnc send an email to Benjamin.A.Matthews@colorado.edu

If any of these commands fail, you may need to source /etc/profile to get the necessary environment variables (this should be fixed soon)

VirtualGL has trouble with some threaded programs. If your OpenGL program exhibits segmentation faults or other issues, this could be the problem. Check back for the solution later.

If the given password is rejected you can run stop_vnc.sh and restart to get a new one. Occasionally the random password generator may generate passwords which VNC doesn't like.

If VirtualGL complains about not being able to get a 24bit FB config either vglconnect to another VirtualGL enabled server or complain to Benjamin.A.Matthews@Colorado.edu

If your VNC connection is very slow, you might want to try changing the compression and encoding options. See your vncviewer's documentation or try this
vncviewer -encodings tight -quality 6 -compresslevel 6
If you have trouble with text distortion try adding
-nojpeg

If you're running OSX and see an error about Zlib, try changing your compression settings (maximum quality usually works) or use a different client. RealVNC and certain versions of ChickenOfTheVNC both exhibit this issue. The latest build of TigerVNC should work reliably, as does the Java based TightVNC client.

VNC

2012-11-01T18:00:45Z

Matthb2:

VNC is a tool which projects a GUI session over the network. If may be useful if you want to use GUI tools remotely when X forwarding performs poorly.

'''Warning: This is still being tested and should NOT be considered stable (portal0 may be rebooted without warning)'''
'''Warning: The vnc password is transmitted in clear text over the network and should not be considered secure'''

Portal0 is designated to host VNC sessions.

You can start a session as follows:

ssh jumpgate-phasta.colorado.edu
ssh portal0
source /etc/profile
start_vnc.sh

And follow the directions

(You may want to remember your password and port number so that you can reuse your session)

When you are done, end your session by
source /etc/profile
stop_vnc.sh

== OpenGL ==

Portal0 is equipped with a VirtualGL install which will allow you to use OpenGL programs (which do not use pthreads)

Simply wrap your OpenGL program with the "vglrun" command
vlgrun glxgears

If you have access to another VirtualGL server you can connect to it first (Portal0 doesn't have a particularly fast graphics processor)
vglconnect server
vglrun glxgears

Note that VGL uses a number of threads. If you have trouble with vglrun crashing with a message about Thread::Start() make sure you haven't set your stack size too large (remove any ulimit -s or ulimit -n calls from your shell start scripts)

== Clients ==

Portal0 uses TurboVNC from the VirtualGL project, available from http://www.virtualgl.org/Downloads/TurboVNC

Other VNC viewers will also work, such as TightVNC and RealVNC

== View Only Mode ==

To share your desktop with another user in view only mode set a view only password
by running
vncpasswd

Have the other user connect in the same way you would but have them set their viewer to be in view only mode and use your view only password. Typically this is done as follows:
vncviewer -viewonly

== Windows ==
The PuTTY SSH client can handle ssh tunneling on Windows based machines. You can download it here: http://www.chiark.greenend.org.uk/~sgtatham/putty/

When you open putty, enter jumpgate-phasta.colorado.edu as in the Host Name box. Then click the + button next to SSH on the left pane (to expand the SSH tree node). Choose the Tunnels page. The start_vnc.sh script should tell you to run "ssh -L????:portal0:???? jumpgate-phasta.colorado.edu" on your machine. Enter the number between the -L and the first colon in the "Source port" box. Enter the rest in the Destination box (starting with portal0) and '''click the add button'''. Then click "Open" and login as normal. You will then be able to use a vncviewer as instructed by the script.

Example:

The script says:
ssh -L5905:portal0:5900 jumpgate-phasta.colorado.edu
enter 5905 in the Source port box
enter portal0:5900 in the destination box.

Try using this viewer utility
http://www.tightvnc.com/download/1.3.10/tightvnc-1.3.10_x86_viewer.zip

== Web Based Viewer ==

If you can't or don't want to install a VNC viewer you can use a Java based one. You will need a JVM and a Java browser plugin. You will also need the port that the start_vnc script assigned you to be free on your local computer

Forward your session through jumpgate as before before, adding a second port, 580n. For example, if the script tells you to

ssh -L5905:portal0:5902 jumpgate-phasta.colorado.edu you should
ssh -L5902:portal0:5902 -L5802:portal0:5802 jumpgate-phasta.colorado.edu
Then point your browser to http://localhost:5802 and log in with the password specified by the script when prompted. (Replace 2 with the value specified by the script)

== Changing the Size (Resolution) of an Existing Session ==

You can usually use the "xrandr" tool to change the resolution of a running vnc session. First you'll need to know your session's display number (this should be the last digit or two of the port number). For example, if your VNC session is running on port 5902, then your screen number should be :2. For this example, we'll use screen 2.

Once you know your screen number, you can see the list of supported modes as follows:
xrandr -display :2

Once you pick the one you want (generally the same size or smaller than the native resolution of your client), you can choose it by running a command like
xrandr -s 1400x1050 -display :2

(this example will set the resolution to 1400 pixels by 1050 pixels)

You'll probably be disconnected at this point, but when you reconnect your screen size should be changed (hopefully without crashing your running programs).

== Finding an Existing Session ==
Run:
/opt/vnc_script/findsession.sh

Which will return the shortened port number of each of your currently running sessions.

== Troubleshooting ==

If you have used vncserver (It doesn't matter which version) on a SCOREC machine before, you will need to clear your vnc settings for the script to work. You can do this by running rm -rf ~/.vnc

stop_vnc.sh may display some errors; this is normal.

If you have trouble deleting ~/.vnc send an email to Benjamin.A.Matthews@colorado.edu

If any of these commands fail, you may need to source /etc/profile to get the necessary environment variables (this should be fixed soon)

VirtualGL has trouble with some threaded programs. If your OpenGL program exhibits segmentation faults or other issues, this could be the problem. Check back for the solution later.

If the given password is rejected you can run stop_vnc.sh and restart to get a new one. Occasionally the random password generator may generate passwords which VNC doesn't like.

If VirtualGL complains about not being able to get a 24bit FB config either vglconnect to another VirtualGL enabled server or complain to Benjamin.A.Matthews@Colorado.edu

If your VNC connection is very slow, you might want to try changing the compression and encoding options. See your vncviewer's documentation or try this
vncviewer -encodings tight -quality 6 -compresslevel 6
If you have trouble with text distortion try adding
-nojpeg

If you're running OSX and see an error about Zlib, try changing your compression settings (maximum quality usually works) or use a different client. RealVNC and certain versions of ChickenOfTheVNC both exhibit this issue. The latest build of TigerVNC should work reliably, as does the Java based TightVNC client.

MATLAB

2012-11-01T01:27:57Z

Matthb2:

[[Category:Software]]

Matlab is installed only on Viz001 and Viz002 (since we only have node-locked licenses). Several recent versions are installed in /opt/MATLAB. Currently, the full path to the latest version is:

/opt/MATLAB/R2012b/bin/matlab

The licenses expire periodically, but can be renewed. If you need an older version and find that the license has expired, please email Benjamin.A.Matthews@Colorado.edu

MATLAB

2012-11-01T01:27:13Z

Matthb2:

[[Category:Software]]

Matlab is installed only on Viz001 and Viz002 (since we only have node-locked licenses). Several versions are installed in /opt/MATLAB. Currently, the full path to the latest version is:

/opt/MATLAB/R2012b/bin/matlab

The licenses expire periodically, but can be renewed. If you need an older version and find that the license has expired, please email Benjamin.A.Matthews@Colorado.edu

VNC

2012-10-30T01:19:46Z

Matthb2: /* Troubleshooting */

VNC is a tool which projects a GUI session over the network. If may be useful if you want to use GUI tools remotely when X forwarding performs poorly.

'''Warning: This is still being tested and should NOT be considered stable (portal0 may be rebooted without warning)'''
'''Warning: The vnc password is transmitted in clear text over the network and should not be considered secure'''

Portal0 is designated to host VNC sessions.

You can start a session as follows:

ssh jumpgate-phasta.colorado.edu
ssh portal0
source /etc/profile
start_vnc.sh

And follow the directions

(You may want to remember your password and port number so that you can reuse your session)

When you are done, end your session by
source /etc/profile
stop_vnc.sh

== OpenGL ==

Portal0 is equipped with a VirtualGL install which will allow you to use OpenGL programs (which do not use pthreads)

Simply wrap your OpenGL program with the "vglrun" command
vlgrun glxgears

If you have access to another VirtualGL server you can connect to it first (Portal0 doesn't have a particularly fast graphics processor)
vglconnect server
vglrun glxgears

Note that VGL uses a number of threads. If you have trouble with vglrun crashing with a message about Thread::Start() make sure you haven't set your stack size too large (remove any ulimit -s or ulimit -n calls from your shell start scripts)

== Clients ==

Portal0 uses TurboVNC from the VirtualGL project, available from http://www.virtualgl.org/Downloads/TurboVNC

Other VNC viewers will also work, such as TightVNC and RealVNC

== View Only Mode ==

To share your desktop with another user in view only mode set a view only password
by running
vncpasswd

Have the other user connect in the same way you would but have them set their viewer to be in view only mode and use your view only password. Typically this is done as follows:
vncviewer -viewonly

== Windows ==
The PuTTY SSH client can handle ssh tunneling on Windows based machines. You can download it here: http://www.chiark.greenend.org.uk/~sgtatham/putty/

When you open putty, enter jumpgate-phasta.colorado.edu as in the Host Name box. Then click the + button next to SSH on the left pane (to expand the SSH tree node). Choose the Tunnels page. The start_vnc.sh script should tell you to run "ssh -L????:portal0:???? jumpgate-phasta.colorado.edu" on your machine. Enter the number between the -L and the first colon in the "Source port" box. Enter the rest in the Destination box (starting with portal0) and '''click the add button'''. Then click "Open" and login as normal. You will then be able to use a vncviewer as instructed by the script.

Example:

The script says:
ssh -L5905:portal0:5900 jumpgate-phasta.colorado.edu
enter 5905 in the Source port box
enter portal0:5900 in the destination box.

Try using this viewer utility
http://www.tightvnc.com/download/1.3.10/tightvnc-1.3.10_x86_viewer.zip

== Web Based Viewer ==

If you can't or don't want to install a VNC viewer you can use a Java based one. You will need a JVM and a Java browser plugin. You will also need the port that the start_vnc script assigned you to be free on your local computer

Forward your session through jumpgate as before before, adding a second port, 580n. For example, if the script tells you to

ssh -L5905:portal0:5902 jumpgate-phasta.colorado.edu you should
ssh -L5902:portal0:5902 -L5802:portal0:5802 jumpgate-phasta.colorado.edu
Then point your browser to http://localhost:5802 and log in with the password specified by the script when prompted. (Replace 2 with the value specified by the script)

== Changing the Size (Resolution) of an Existing Session ==

You can usually use the "xrandr" tool to change the resolution of a running vnc session. First you'll need to know your session's display number (this should be the last digit or two of the port number). For example, if your VNC session is running on port 5902, then your screen number should be :2. For this example, we'll use screen 2.

Once you know your screen number, you can see the list of supported modes as follows:
xrandr -display :2

Once you pick the one you want (generally the same size or smaller than the native resolution of your client), you can choose it by running a command like
xrandr -s 1400x1050 -display :2

(this example will set the resolution to 1400 pixels by 1050 pixels)

You'll probably be disconnected at this point, but when you reconnect your screen size should be changed (hopefully without crashing your running programs).

== Troubleshooting ==

If you have used vncserver (It doesn't matter which version) on a SCOREC machine before, you will need to clear your vnc settings for the script to work. You can do this by running rm -rf ~/.vnc

stop_vnc.sh may display some errors; this is normal.

If you have trouble deleting ~/.vnc send an email to Benjamin.A.Matthews@colorado.edu

If any of these commands fail, you may need to source /etc/profile to get the necessary environment variables (this should be fixed soon)

VirtualGL has trouble with some threaded programs. If your OpenGL program exhibits segmentation faults or other issues, this could be the problem. Check back for the solution later.

If the given password is rejected you can run stop_vnc.sh and restart to get a new one. Occasionally the random password generator may generate passwords which VNC doesn't like.

If VirtualGL complains about not being able to get a 24bit FB config either vglconnect to another VirtualGL enabled server or complain to Benjamin.A.Matthews@Colorado.edu

If your VNC connection is very slow, you might want to try changing the compression and encoding options. See your vncviewer's documentation or try this
vncviewer -encodings tight -quality 6 -compresslevel 6
If you have trouble with text distortion try adding
-nojpeg

If you're running OSX and see an error about Zlib, try changing your compression settings (maximum quality usually works) or use a different client. RealVNC and certain versions of ChickenOfTheVNC both exhibit this issue. The latest build of TigerVNC should work reliably, as does the Java based TightVNC client.