SourceWiki - User contributions [en]

BISMG

2009-11-11T16:32:00Z

Asis:

=Bristol Ice Sheet Modellers Group!=

This is where Tony Payne's group working on ice sheet modelling share progress updates and ideas and other useful information.

'''Members please [[BISMG:Main | click here]]'''

Asis

2009-11-11T14:58:44Z

Asis:

[[Category:Projects]]

= ASIS - Amundsen Sea embayment project Ice Sheet model development =

'''Purpose'''
The title comes from ASEP, the Amundsen Sea Embayment Project.
This wiki page is intended as a forum for discussing and resolving ice sheet model development issues and data available relating to Tony Payne's WAIS project and ASEP.

'''Access'''
Most of this wiki area is currently accessible only to developers involved in the relevant projects. If you think you should have access then please contact Rupert Gladstone (r.gladstone@bris.ac.uk) or Tony Payne in the first instance.

'''Members please [[ASIS:Main | click here]]'''

==Third Party Tools ==

* [[CHOMBO]]
* [[SAMRAI]]
* [[VisIt]]
* [[ChomboVis]]
* [[Xming]]

CHOMBO

2008-11-12T12:43:29Z

Asis: added section on contents of d/f/o/p directories

CHOMBO

=Introduction=

=Installation=

This page describes what I (Gethin) did to install and run CHOMBO. In the first instance, I worked on dyln (an x86_64 machine) and used the GNU C and Fortran compilers (gcc, g++ and gfortran).

First we will look at the prerquisites, an MPI implementation and HDF5, and then CHOMBO itself.

==MPICH v1.2.6==

Only an MPI 1.2 compliant C binding is required to run CHOMBO in parallel. There are problems getting gfortran to work with both MPICH v1.2.5 and v1.2.6, so I will omit it here. '''Beware''', however of picking up e.g. the Sun fortran compiler as '''f77''' and '''f90''' and thus getting a mixed compiler MPICH build.

Get tar ball:
<pre>
wget ftp://ftp.mcs.anl.gov/pub/mpi/old/mpich-1.2.6.tar.gz
</pre>

Treating dylan as an SMP machine (multi-core with shared memory), we will build a shared memory MPI installation:

<pre>
./configure --prefix=/gsb6/ggdagw/mpich/mpich-1.2.6/ch_shmem --with-device=ch_shmem -cc=gcc -c++=g++ \
-fc=gfortran -f90=gfortran -cflags="-D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64" \
>& config.out
make
make testing
make install
</pre>

The cflags enable files > 2GB.

'''Note''' that Fortran binding will not be built, as MPICH will complain that it can't access the command line through gfortran. '''Also''' that I needed to copt '''mpicxx''' to '''mpiCC''' in the install directory, for some reason..

==HDF5 v1.4.4==

Get from:

<pre>
ftp://hdf.ncsa.uiuc.edu/HDF5/prev-releases
</pre>

===For Serial Build===

<pre>
./configure --prefix=/gsb6/ggdagw/hdf5/hdf5-1.4.4/serial --enable-production
</pre>

===For Parallel Build===

Tested MPI-IO with the program Sample_mpio.c from PHDF5 instructions (appendix) in conjunction with shmem MPI build and tests passed OK.

Straight from the box, we would have a broken build, due to problems with mpicc and DL_OPEN support. So, we will make a cheeky edit. In the file '''config/commence.in''', change the line that defines the LT_LINK_EXE variable to remove the '''-dlopen self -rpath $(libdir)''' options.

Note that we've disabled linking against shared libraries. We could have gone the other way and added '''-fPIC'' to the build flags.

Now we configure and build:

<pre>
CC=/gsb6/ggdagw/mpich/mpich-1.2.6/ch_shmem/bin/mpicc ./configure --disable-shared \
--prefix=/gsb6/ggdagw/hdf5/hdf5-1.4.4/parallel
make
make check
make install
</pre>

==HDF5 v1.6.7==

We could use this too. For a parallel build, for example:

<pre>
CC=/gsb6/ggdagw/mpich/mpich-1.2.6/ch_shmem/bin/mpicc ./configure --disable-shared \
--prefix=/gsb6/ggdagw/hdf5/hdf5-1.6.7/parallel
make
make check
make install
</pre>

Seems to be OK.

==CHOMBO==
The Oct07 release is installed in '''/gsb6/ggdagw/chombo/Chombo-2.0'''.

===Without HDF5===
lib/mk/Make.defs.local:
<pre>
DIM = 2
DEBUG = TRUE
OPT = TRUE
PRECISION = DOUBLE
PROFILE = FALSE
CXX = g++
FC = gfortran
MPI = FALSE
USE_HDF = FALSE
</pre>

make lib
make test
make run

Looks like the tests pass '''BUT uses -m32''' during compilation and so a 32bit executable results. This is fine here (since x86_64 will also handle 32bit exes), but it causes a problem when we try and link against 64bit dependencies, such as HDF5 (see below for remedy).

===With HDF5 compiled in serial mode===

<pre>
USE_64 = TRUE
</pre>

adds -m64 to the GNU compiler flags and so object code is created for the x86_64 architecture, and so it will link against the HDF libraries which are built for x86_64. This is not what the documentation says the makefile variable is for! Hey ho. Add it in.

* e.g. export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/gsb6/ggdagw/hdf5/hdf5-1.4.4/serial/lib

required to find shared object files, else tests will not run. Tests look OK for both v1.4.4 and v1.6.7 of HDF.

===With MPI and parallel HDF5===

Add in to Make.defs.local:

<pre>
MPICXX = /gsb6/ggdagw/mpich/mpich-1.2.6/ch_shmem/bin/mpiCC
HDFMPIINCFLAGS= -I/gsb6/ggdagw/hdf5/hdf5-1.4.4/parallel/include
HDFMPILIBFLAGS= -L/gsb6/ggdagw/hdf5/hdf5-1.4.4/parallel/lib -lhdf5 -lz
</pre>

<pre>
cd chombo/lib
make lib
make test
make run
</pre>

Tests look to pass OK for both HDF5v1.4.4 and v1.6.7.

===Running the AMRUpwind example from Gethin's build===

* Ensure that '''/gsb6/ggdagw/mpich/mpich-1.2.6/ch_shmem/bin''' is in your path
* copy '''~ggdagw/chombo/Chombo-2.0/example''' to your location of choice
* cd AMRUpwind
* edit:
** '''GNUmakefile''' such that: '''CHOMBO_HOME = ../../chombo/Chombo-2.0/lib'''
** '''exec/GNUmakefile''' such that: '''CHOMBO_HOME = ../../../chombo/Chombo-2.0/lib'''
* make clean
* make example
* make run

===Useful informatiomn on files within example===

After compilation, you will find 4 directories created within the example directory. Each contains subdirectories based on the particular build (e.g., 2d.Linux.64.mpiCC.gfortran.DEBUG.OPT.MPI/). These are:

* '''d''' which contains paths for any files used in the compilation; most usefully .H etc files.
* '''f''' which contains fortan code after it has been parsed; particularly useful in the case of ChF files (.f).
* '''o''' which contains usual .o objects.
* '''p''' which also contains parsed versions of any fortran code (.cpre is same as .f above).

===Changes to Makefiles for Fortran90===

In '''Chombo-2.0/lib/mk/Make.example''':

<pre>
src_extensions := .cpp .ChF .F .f .c .f90
vpath %.cpp $(src_dirs)
vpath %.ChF $(src_dirs)
vpath %.F $(src_dirs)
vpath %.f $(src_dirs)
vpath %.c $(src_dirs)
vpath %.f90 $(src_dirs)
</pre>

In '''Chombo-2.0/lib/mk/Make.rules''':

line 104:
<pre>
src_wildcard := *.cpp *.ChF *.F *.f *.f90
</pre>

add after line ~350:
<pre>
o/$(config)/%.o : %.f90 d/$(config)/%.d
$(QUIET)$(FC) $(FFLAGS) $(XTRAFFLAGS) $(fcompflag) $< $(fobjflag)$@
</pre>

add after line ~413:
<pre>
d/$(config)/%.d : %.f90 d/$(config)/.dummy
@if [ x"$(QUIET)" != x"@" ]; then echo Depending $< ...; fi
</pre>

Tested '''example/expHeat/parVersion''' by replacing '''heatfort.F''' with '''heatfort.f90'''.

VisIt

2008-10-31T16:32:09Z

Asis:

==Installing [https://wci.llnl.gov/codes/visit/home.html VisIt] 1.10.0==

These are notes from Rupert Gladstone. I would need to re-build visit to ensure that these notes are correct.

1. Create the directory in which you wish to install VisIt, and cd to this
directory.

2. Download the [https://wci.llnl.gov/codes/visit/1.10.0/build_visit build VisIt] script.

3. Download the VisIt 1.10.0 sources from the [https://wci.llnl.gov/codes/visit/source.html downloads] page.

4. Under Setup in the [https://wci.llnl.gov/codes/visit/1.10.0/build_visit build VisIt] script
is a list of required 3rd party software. Download all the 'must have' tarballs and also
HDF5, NetCDF, szip. These can be downloaded from the bottom of the
[https://wci.llnl.gov/codes/visit/source.html downloads]
page.

5. (optional) If you want to use an existing installation of the 3rd party software
(note that that in some cases VisIt requires older versions) you can
force this with [[VisIt:compile_hack | this hack]] (uses Python as an example).

6. Run the [https://wci.llnl.gov/codes/visit/1.10.0/build_visit build VisIt] script.

Further notes:

I also had to download Imaging-1.1.6.tar.gz from
[http://effbot.org/downloads/ here], prompted by a message in the build log.

Note that this should give a valid install of VisIt, but VisIt will still not function properly
when used remotely via ssh/exceed. This is because exceed does not support openGL. See also this
[http://www.linuxforums.org/forum/linux-desktop-x-windows/32497-glx-extension-missing.html Linux forum comment]
and the
[http://connectivity.hummingbird.com/products/nc/exceed/index.html?cks=y exceed website]
for more info.
It would appear that exceed3d could be purchased to get round this problem.

VisIt

2008-10-31T15:22:46Z

Asis:

==Installing [https://wci.llnl.gov/codes/visit/home.html VisIt] 1.10.0==

These are notes from Rupert Gladstone. I would need to re-build visit to ensure that these notes are correct.

Download the [https://wci.llnl.gov/codes/visit/1.10.0/build_visit build VisIt] script.

Download the VisIt sources from the [https://wci.llnl.gov/codes/visit/source.html downloads] page.

Under Setup in the [https://wci.llnl.gov/codes/visit/1.10.0/build_visit build VisIt] script
is a list of required 3rd party software. Download all the 'must have' tarballs and
HDF5, NetCDF, szip. These can be downloaded from the bottom of the
[https://wci.llnl.gov/codes/visit/source.html VisIt downloads]
page.

I also had to download Imaging-1.1.6.tar.gz from
[http://effbot.org/downloads/ here], prompted by a message in the build log.

If you want to use an existing installation of the 3rd party software
(note that that in some cases VisIt requires older versions) you can
force this with the following [[VisIt:compile_hack | hack]] (uses Python as an example):

Run the [https://wci.llnl.gov/codes/visit/1.10.0/build_visit build VisIt] script.

Note that this should give a valid install of VisIt, but VisIt will still not functiona properly
when used remotely via ssh/exceed. This is because exceed does not support openGL. See also this
[http://www.linuxforums.org/forum/linux-desktop-x-windows/32497-glx-extension-missing.html Linux forum comment]
and the
[http://connectivity.hummingbird.com/products/nc/exceed/index.html?cks=y exceed website]
for more info.
It would appear that exceed3d could be purchased to get round this problem.

VisIt:compile hack

2008-10-31T15:22:36Z

Asis:

If you want to use an existing installation of the 3rd party software
(note that that in some cases VisIt requires older versions) you can
force this with the following hack (uses Python as an example):

From the directory you run build_visit from, run the
command:

mkdir -p visit/python/2.5/linux-x86_64_gcc-4.1.2 (last bit is architecture/compiler dependant)

This will cause build_visit to think python is already installed,
skipping the compile/install of it. However, after build_visit
completes, you'll have to change your `host`.conf. Simply change the

PYDIR=/some/long/directory/name

line to:

PYDIR=/usr

This will cause VisIt to use your system's python.

VisIt:compile hack hack

2008-10-31T15:21:47Z

Asis:

VisIt

2008-10-31T15:21:36Z

Asis:

==Installing [https://wci.llnl.gov/codes/visit/home.html VisIt] 1.10.0==

These are notes from Rupert Gladstone. I would need to re-build visit to ensure that these notes are correct.

Download the [https://wci.llnl.gov/codes/visit/1.10.0/build_visit build VisIt] script.

Download the VisIt sources from the [https://wci.llnl.gov/codes/visit/source.html downloads] page.

Under Setup in the [https://wci.llnl.gov/codes/visit/1.10.0/build_visit build VisIt] script
is a list of required 3rd party software. Download all the 'must have' tarballs and
HDF5, NetCDF, szip. These can be downloaded from the bottom of the
[https://wci.llnl.gov/codes/visit/source.html VisIt downloads]
page.

I also had to download Imaging-1.1.6.tar.gz from
[http://effbot.org/downloads/ here], prompted by a message in the build log.

If you want to use an existing installation of the 3rd party software
(note that that in some cases VisIt requires older versions) you can
force this with the following [[VisIt:compile_hack hack]] (uses Python as an example):

From the directory you run build_visit from, run the
command:

mkdir -p visit/python/2.5/linux-x86_64_gcc-4.1.2 (last bit is architecture/compiler dependant)

This will cause build_visit to think python is already installed,
skipping the compile/install of it. However, after build_visit
completes, you'll have to change your `host`.conf. Simply change the

PYDIR=/some/long/directory/name

line to:

PYDIR=/usr

This will cause VisIt to use your system's python.

Run the [https://wci.llnl.gov/codes/visit/1.10.0/build_visit build VisIt] script.

Note that this should give a valid install of VisIt, but VisIt will still not functiona properly
when used remotely via ssh/exceed. This is because exceed does not support openGL. See also this
[http://www.linuxforums.org/forum/linux-desktop-x-windows/32497-glx-extension-missing.html Linux forum comment]
and the
[http://connectivity.hummingbird.com/products/nc/exceed/index.html?cks=y exceed website]
for more info.
It would appear that exceed3d could be purchased to get round this problem.

Asis

2008-10-31T14:46:21Z

Asis:

[[Category:Projects]]

= ASIS - Amundsen Sea embayment project Ice Sheet model development =

'''Purpose'''
The title comes from ASEP, the Amundsen Sea Embayment Project.
This wiki page is intended as a forum for discussing and resolving ice sheet model development issues and data available relating to Tony Payne's WAIS project and ASEP.

'''Access'''
Most of this wiki area is currently accessible only developers involved in the relevant projects. If you think you should have access then please contact Rupert Gladstone (r.gladstone@bris.ac.uk) or Tony Payne in the first instance.

'''Members please [[ASIS:Main | click here]]'''

==Third Party Tools ==

* [[CHOMBO]]
* [[SAMRAI]]
* [[VisIt]]

File:Flotation m917 17.jpg

2008-10-31T14:44:41Z

Asis:

File:Flotation m917 m.jpg

2008-10-31T14:30:12Z

Asis:

File:Flotation m917.jpg

2008-10-30T10:05:54Z

Asis:

File:Flotation m2.jpg

2008-10-30T09:37:39Z

Asis:

File:Flotation m.jpg

2008-10-29T14:17:22Z

Asis:

File:Combthk.jpg

2008-10-29T12:03:19Z

Asis:

File:Agasea datasources2.jpg

2008-10-29T12:03:02Z

Asis:

File:Allthick sm.jpg

2008-10-29T12:02:16Z

Asis:

File:Allthick unsm.jpg

2008-10-29T12:01:56Z

Asis:

File:Flotation.jpg

2008-10-28T16:08:18Z

Asis:

File:Combbed.jpg

2008-10-28T16:07:27Z

Asis: