UV-CDAT versions installed by JYP

This page describes versions of UV-CDAT installed by JYP, up to 2.1.0 For more recent versions, 2.8.0 and later, check the UV-CDAT conda versions installed by JYP page

Official list of available versions

Useful links

UV-CDAT @ github

UV-CDAT issues @ github

2.1.0

Official details :

cdat_multi configuration version: 13

Available configurations

Machine	Config	Python/date	Notes
LSCE	LSCE_13	2.7.8, Jan 22 2015	Red Hat Enterprise Linux Server release 6.6 (Santiago) Used system's cmake (2.8.12.2) and the same recompiled Qt (4.8.5) used for uv-cdat 1.5.1
ciclad	ciclad_13	2.7.8, Feb 5 2015	Scientific Linux release 6.6 (Carbon) Used system's cmake (2.8.12.2) and the same recompiled Qt (4.8.5) used for uv-cdat 1.5.1
VirtualBox FC20	VB_13	2.7.8, Feb 2 2015	Fedora release 20 (Heisenbug) Used system's cmake (2.8.12.2) and Qt (4.8.6-18.fc20.x86_64)

Log files

Machine	make	ctest
LSCE	txt	txt
ciclad	txt	txt
VirtualBox FC20	txt	txt

make summary

--- WARNING ---
2 Packages reported as FAILED, see logs
contrib/pyclimate
contrib/MSU

ctest summary

In a new installation, test #343 (diags_test_01) will fail the first time ctest is called because the test data in the UVCMETRICS_TEST_DATA_DIRECTORY directory is not available

99% tests passed, 1 tests failed out of 343
Total Test time (real) = 478.10 sec
The following tests FAILED:
343 - diags_test_01 (Failed)
Errors while running CTest

If you run ctest -D Experimental, the test data is downloaded and all tests pass!

100% tests passed, 0 tests failed out of 343
Total Test time (real) = 697.55 sec

ccmake options

ccmake -D GIT_PROTOCOL=git:// -DCDAT_BUILD_MODE=DEFAULT -DCDAT_BUILD_CMOR=ON -D CMAKE_INSTALL_PREFIX=$CDAT_INSTALL -D CDAT_BUILD_BASEMAP=ON -D CDAT_BUILD_MATPLOTLIB=ON -D CDAT_BUILD_SCIENTIFICPYTHON=ON -D CDAT_BUILD_SCIKITS=ON -D CDAT_BUILD_SHAPELY=ON -D CDAT_BUILD_JINJA2=ON -D CDAT_BUILD_PYGMENTS=ON -D CDAT_BUILD_PYZMQ=ON -D CDAT_BUILD_SPHINX=ON -D CDAT_BUILD_TORNADO=ON -D UVCMETRICS_TEST_DATA_DIRECTORY=/<some_scratch_directory>/uvcmetrics_test_data -D CDAT_BUILD_LIBXML2=OFF -D CDAT_USE_SYSTEM_LIBXML2=ON -D CDAT_BUILD_LIBXSLT=OFF -D CDAT_USE_SYSTEM_LIBXSLT=ON $CDAT_MAIN_DIR

BUILD_TESTING

Note: we have not explicitly requested to turn on the testing, because it is supposed to be ON by default

GIT_PROTOCOL

We have used -D GIT_PROTOCOL=git://. See the 1.5.1 options for more details

CDAT_BUILD_MODE

We want to get most of the useful stuff. Check Install from source command line options for more details

-DCDAT_BUILD_MODE=DEFAULT

CDAT_BUILD_CMOR

We need to experiment with CMOR…

-DCDAT_BUILD_CMOR=ON

Misc options

What do we want?	ccmake option
basemap	-D CDAT_BUILD_BASEMAP=ON
matplotlib	-D CDAT_BUILD_MATPLOTLIB=ON
scientificpython	-D CDAT_BUILD_SCIENTIFICPYTHON=ON
sckikits if we want to experiment later with scikit image	-D CDAT_BUILD_SCIKITS=ON
shapely seems useful for dealing with data on irregular grids	-D CDAT_BUILD_SHAPELY=ON
ipython notebook some users may want to play with that	-D CDAT_BUILD_JINJA2=ON -D CDAT_BUILD_PYGMENTS=ON -D CDAT_BUILD_PYZMQ=ON -D CDAT_BUILD_SPHINX=ON -D CDAT_BUILD_TORNADO=ON

UVCMETRICS_TEST_DATA_DIRECTORY

-D UVCMETRICS_TEST_DATA_DIRECTORY=/<some_scratch_directory>/uvcmetrics_test_data

The content of this directory is required for ctest Test #343: diags_test_01 to pass. Strangely, it is only downloaded when you run ctest -D Experimental, so ctest (without -D Experimental) fails test #343 the first time…

LIBXML2 & LIBXSLT

We have tried to use the system's installed libxml2 and libxslt libraries by using the following options:

-D CDAT_BUILD_LIBXML2=OFF -D CDAT_USE_SYSTEM_LIBXML2=ON -D CDAT_BUILD_LIBXSLT=OFF -D CDAT_USE_SYSTEM_LIBXSLT=ON

Unfortunately, uvcdat still compiles the new version of the libraries, and then the system's cmake gets confused and we get lots of warning messages of the following kind each time cmake is called. See issue 444 for more details

cmake --version
cmake: /home/share/unix_files/cdat/versions/cdat_install_uv-2.1.0_x86_64_gcc4_13/Externals/lib/libxml2.so.2: no version information available (required by /usr/lib64/libarchive.so.2)
cmake: /home/share/unix_files/cdat/versions/cdat_install_uv-2.1.0_x86_64_gcc4_13/Externals/lib/libxml2.so.2: no version information available (required by /usr/lib64/libarchive.so.2)
cmake: /home/share/unix_files/cdat/versions/cdat_install_uv-2.1.0_x86_64_gcc4_13/Externals/lib/libxml2.so.2: no version information available (required by /usr/lib64/libarchive.so.2)
cmake: /home/share/unix_files/cdat/versions/cdat_install_uv-2.1.0_x86_64_gcc4_13/Externals/lib/libxml2.so.2: no version information available (required by /usr/lib64/libarchive.so.2)
cmake version 2.8.12.2

System specific notes

VB_13 installation

During the compilation, make fails because of the VTK/Mesa/OpenGL/FedoraCore20 related problem detailed in issue 983
Solution: uncomment the #define GLX_GLXEXT_LEGACY line in build/build/VTK/Rendering/OpenGL/vtkXOpenGLRenderWindow.cxx and restart the compilation

After resuming the compilation with the above patch, the compilation fails because of a CMOR related make/Makefile error described in CMOR issue 14
Solution: indent lines 156 and 157 with a Tab instead of 8 spaces in build/build/cmor/Makefile and restart the compilation

Disk space

The following disk space was required for the installation

Machine	-A- cmake compile (1)	-B- cmake install	-C- qt compile (1)	-D- qt install	-E- cdat src (2?)	-F- cdat build (2)	-G- cdat install (2)	-H- Externals (3) Sub-dir of install	-I- Installation space (4)	-J- Final space (5)
LSCE	0 (6)	0 (6)	1.6G	451M
ciclad	0 (6)	0 (6)	?	455M	578M	4.7G	1.6G	545M	7.3	2.0
VirtualBox FC20	0 (6)	0 (6)	0 (6)	0 (6)	565M	5.0G	1.7G	511M	7.3	1.7

Notes:

(1) The compilation directories of cmake and Qt can be removed once the installation of cmake/Qt is finished (ie can be removed before starting with uv-cdat)

(2) The packages required for the GUI, and Paraview, were not installed and would probably require even more space

(3) The size of this directory can change depending on the dependencies use from what's already available on the system (xml2 and xslt in this installation) and what we recompile

(4) Sum of the columns, if we erase the A/C directories: B + D + E + F + G

(5) Sum of the columns, if we erase the B/E/F directories: D + G

(6) We used the version available on the system (that was enough up-to-date)

2.0.0

Official details :

cdat_multi configuration version: 12

2.0.beta

Official details : 2.0.beta

cdat_multi configuration version: 11

Available configurations

Machine	Config	Python/date	Notes
LSCE	LSCE_11	2.7.7, Aug 1 2014	Used the same recompiled cmake and Qt as for 1.5.1
ciclad	ciclad_11-ng	2.7.7, Aug 4 2014	Used the same recompiled cmake and Qt as for 1.5.1

Log files

Machine	make	ctest
LSCE	txt	txt
ciclad-ng	txt	txt

make summary

2 Packages reported as FAILED, see logs
contrib/pyclimate
contrib/MSU

ctest summary

53% tests passed, 35 tests failed out of 74
Total Test time (real) = 1020.63 sec
The following tests FAILED:
2 - cdms_test (Failed)
3 - cdms_verify (Failed)
4 - cdms_load_and_plot_axis_variable (Failed)
5 - run_uvcdat_gui_tests (Failed)
6 - test177_regrid_mask (Failed)
8 - testDoutriaux (Failed)
9 - testMarvel (Failed)
10 - testUnits (Failed)
11 - testRaynaud (Failed)
12 - testDateline (Failed)
14 - testDiag (Failed)
15 - testSo2TasACCESSFails (Failed)
16 - testSo2Tas (Failed)
17 - testWrite (Failed)
18 - testMvCdmsRegrid (Failed)
21 - testConserv (Failed)
22 - testEsmfVsLibcf (Failed)
23 - testEsmfInterface1 (Failed)
28 - testTasRegrid (Failed)
30 - testRegrid2 (Failed)
34 - testEsmf_3x4_6x8_Conserve_Masked (Failed)
36 - testMvGenericRegrid (Failed)
37 - testSalinity (Failed)
38 - testEsmfSalinity (Failed)
39 - testEsmf (Failed)
40 - testBergman (Failed)
41 - testDistSrc (Failed)
43 - vcs_verify_import (Failed)
44 - vcs_verify_init (Failed)
45 - vcs_verify_boxfill_basics (Failed)
46 - vcs_verify_proj_basics (Failed)
47 - vcs_verify_fillarea_basics (Failed)
66 - CDMS_Test_17 (Failed)
68 - CDMS_Test_multiple_formats (Failed)
74 - diags_test_01 (Failed)

ccmake options

ccmake -D GIT_PROTOCOL=git:// -D CDAT_BUILD_PARALLEL=OFF -D CDAT_BUILD_LIBXML2=OFF -D CDAT_USE_SYSTEM_LIBXML2=ON -D CDAT_BUILD_LIBXSLT=OFF -D CDAT_USE_SYSTEM_LIBXSLT=ON -D CMAKE_INSTALL_PREFIX=$CDAT_INSTALL $CDAT_MAIN_DIR

Installation environment

LSCE

Same as for 1.5.1

ciclad-ng

Same as for 1.5.1

VirtualBox FC20

Disk space

The following disk space was required for the installation

Extra packages installed

Requests: HTTP for Humans

Web site: http://docs.python-requests.org/en/latest/

Install: pip install requests

1.5.1

Official details : 1.5.1

cdat_multi configuration version: 10

Special warning

The default backend for matplotlib (Agg) could not be used for interactive graphics and we had to manually update the content of the default matplotlibrc

<INSTALL>/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc
#backend : Agg
backend : Qt4Agg

Available configurations

Machine	Config	Python/date	Notes
LSCE	LSCE_10	2.7.4, Apr 23 2014	Had to use recompiled cmake (2.8.12.2) and Qt (4.8.5) because the system ones were too old
ciclad	ciclad_10	FAILED	Linux too old, even when specifying recent gcc44/gfortran44/g++44 compilers, we end up with too many problems, …
ciclad-ng	ciclad_10-ng	2.7.4, Apr 22 2014	Had to use recompiled cmake (2.8.12.2) and Qt (4.8.5) because the system ones were too old
VirtualBox FC20	VB_10

Log files

Machine	make	ctest
LSCE	txt	txt
ciclad
ciclad-ng	txt	txt
VirtualBox FC20	txt	txt

make summary

3 Packages reported as FAILED, see logs
contrib/pyclimate
contrib/MSU
contrib/windspharm

ctest summary

89% tests passed, 8 tests failed out of 71
The following tests FAILED:
1 - run_uvcdat (Failed)
2 - cdms_test (Failed)
3 - cdms_verify (Failed)
4 - cdms_load_and_plot_axis_variable (Failed)
5 - run_uvcdat_gui_tests (Failed)
44 - vcs_test_anim_basic (Failed)
64 - CDMS_Test_18 (Failed)
66 - CDMS_Test_multiple_formats (Failed)
Errors while running CTest

ccmake options

ccmake -D GIT_PROTOCOL=git:// -D CDAT_BUILD_PARALLEL=OFF -D CDAT_BUILD_LIBXML2=OFF -D CDAT_USE_SYSTEM_LIBXML2=ON -D CDAT_BUILD_LIBXSLT=OFF -D CDAT_USE_SYSTEM_LIBXSLT=ON -D CDAT_BUILD_PARAVIEW=OFF -D CDAT_BUILD_GUI=OFF -D CMAKE_INSTALL_PREFIX=$CDAT_INSTALL $CDAT_MAIN_DIR

BUILD_TESTING

If you want to test UV-CDAT with 'ctest' after the build, it must be installed with -D BUILD_TESTING=ON (which seems to be defined by default so we have not added it explicitly to the ccmake options)

GIT_PROTOCOL

It's better to specify explicitly the git protocol to use for downloading submodules in $CDAT_MAINDIR/contrib (-D GIT_PROTOCOL=git:// for all the machines we used), otherwise ccmake gets stuck in a long guru meditation when it's waiting/trying to download external sources.

In order to determine which protocol to use, go to a temporary directory and check by hand which protocol is working. If nothing happens (seems to hang and you have to interrupt with CTRL-C), it's NOT working:

git clone http://github.com/UV-CDAT/scimake.git

git clone git://github.com/UV-CDAT/scimake.git

IF “git clone git” fails, THEN specify '-D GIT_PROTOCOL=http://', otherwise specify '-D GIT_PROTOCOL=git://'

WARNING! WARNING! Check the git protocol overrides remaining from previous CDAT installations with git config –global -l, in remove some lines in ~/.gitconfig if need be…

CDAT_BUILD_PARALLEL

We have used -D CDAT_BUILD_PARALLEL=OFF in order to disable parallelism and avoid potential mpi-related problems

What is really disabled/affected by this option??

LIBXML2 & LIBXSLT

We have used the following options in order to use the xml2/xslt libraries preinstalled on the system and avoid potential compilation problems. As of version 1.5.1, uv-cdat can compile libxml2 if the one available on the system is too old, but the rest of the installation still picks up the old system xml2 library

-D CDAT_BUILD_LIBXML2=OFF -D CDAT_USE_SYSTEM_LIBXML2=ON -D CDAT_BUILD_LIBXSLT=OFF -D CDAT_USE_SYSTEM_LIBXSLT=ON

CDAT_BUILD_GUI

We have to disable the GUI in 1.5.0-1, with -D CDAT_BUILD_GUI=OFF. Otherwise ccmake does not work due to vistrails related problems

CDAT_BUILD_PARAVIEW

Paraview can't be installed, due to R include files not found. Disabling the GUI with -D CDAT_BUILD_GUI=OFF is not enough, so we have to disable it with -D CDAT_BUILD_PARAVIEW=OFF. We then have a problem with pixman being built before freetype so we have to add that pixman depends on freetype

in src/CMake/cdat_modules/pixman_deps.cmake:

set(pixman_deps ${pkgconfig_pkg} ${zlib_pkg})

⇒ set(pixman_deps ${pkgconfig_pkg} ${zlib_pkg} ${freetype_pkg})

Installation environment

LSCE

/etc/redhat-release	Red Hat Enterprise Linux Server release 6.5 (Santiago)
uname -a	Linux asterix1 2.6.32-431.3.1.el6.x86_64 #1 SMP Fri Dec 13 06:58:20 EST 2013 x86_64 x86_64 x86_64 GNU/Linux
gcc	gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4)
gfortran	GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4)
g++	g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4)
Qt	qt-4.6.2-28.el6_5.x86_64 ⇒ had to install 4.8.5
cmake	cmake-2.6.4-5.el6.x86_64 ⇒ had to install 2.8.12.2

ciclad

/etc/redhat-release	CentOS release 5.2 (Final)
uname -a	Linux ciclad1.ipsl.jussieu.fr 2.6.18-348.4.1.el5 #1 SMP Tue Apr 16 15:40:06 EDT 2013 x86_64 x86_64 x86_64 GNU/Linux
gcc44	gcc44 (GCC) 4.4.6 20110731 (Red Hat 4.4.6-3)
gfortran44	GNU Fortran (GCC) 4.4.6 20110731 (Red Hat 4.4.6-3)
g++44	g++44 (GCC) 4.4.6 20110731 (Red Hat 4.4.6-3)
Qt	qt4-4.7.4-0 ⇒ had to install 4.8.5
cmake	cmake-2.6.4-5.el5.2 ⇒ had to install 2.8.12.2

ciclad-ng

/etc/redhat-release	Scientific Linux release 6.5 (Carbon)
uname -a	Linux ciclad-ng.private.ipsl.fr 2.6.32-431.11.2.el6.x86_64 #1 SMP Tue Mar 25 11:15:18 CDT 2014 x86_64 x86_64 x86_64 GNU/Linux
gcc	gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4)
gfortran	GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4)
g++	g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4)
Qt	qt-4.6.2-26.el6_4.x86_64 ⇒ had to install 4.8.5
cmake	cmake-2.6.4-5.el6.x86_64 ⇒ had to install 2.8.12.2

VirtualBox FC20

/etc/redhat-release	Fedora release 20 (Heisenbug)
uname -a	Linux lsce3017.extra.cea.fr 3.13.10-200.fc20.x86_64 #1 SMP Mon Apr 14 20:34:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
gcc	gcc (GCC) 4.8.2 20131212 (Red Hat 4.8.2-7)
gfortran	GNU Fortran (GCC) 4.8.2 20131212 (Red Hat 4.8.2-7)
g++	g++ (GCC) 4.8.2 20131212 (Red Hat 4.8.2-7)
Qt	qt-4.8.5-15.fc20.x86_64
cmake	cmake-2.8.12.2-2.fc20.x86_64

Disk space

The following disk space was required for the installation

Machine	-A- cmake compile (1)	-B- cmake install	-C- qt compile (1)	-D- qt install	-E- cdat src (2?)	-F- cdat build (2)	-G- cdat install (2)	-H- Externals (3) Sub-dir of install	-I- Installation space (4)	-J- Final space (5)
LSCE	230M	69M	1.6G	451M	407M	3.2G	1.1G	372M	5.21G	1.54G
ciclad	?	66M	?	455M	407M	2.8G FAILED	390M FAILED	176M FAILED
ciclad-ng	?	69M	?	449M	407M	3.1G	1.1G	366M	5.10G	1.54G
VirtualBox FC20	0 (6)	0 (6)	0 (6)	0 (6)	407M	3.6G	1.2G	325M	5.20G	1.2G

Notes:

(1) The compilation directories of cmake and Qt can be removed once the installation of cmake/Qt is finished (ie can be removed before starting with uv-cdat)

(2) The packages required for the GUI, and Paraview, were not installed and would probably require even more space

(3) The size of this directory can change depending on the dependencies use from what's already available on the system (xml2 and xslt in this installation) and what we recompile

(4) Sum of the columns, if we erase the A/C directories: B + D + E + F + G

(5) Sum of the columns, if we erase the B/E/F directories: D + G

(6) We used the version available on the system (that was enough up-to-date)

1.5.0

Official details : n/a

cdat_multi configuration version: 09

Check the installation details of 1.5.1 above. Installation tests of 1.5.0 were stopped as soon as 1.5.1 was available

Machine	Config	Notes
LSCE	LSCE_09

1.1.0

Official details : n/a

cdat_multi configuration version: 08

Machine	Config	Python/date	Notes
LSCE	LSCE_08	2.7.3, Nov 13 2012
TGCC	curie_08	2.7.3, Oct 29 2012	The only CDAT available @ TGCC as of April 2014

6.0.0.alpha

Official details : n/a

cdat_multi configuration version: 02

Machine	Config	Python/date	Notes
ciclad	ciclad_02	2.7.1, Aug 12 2011

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