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other:uvcdat:installed

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

Installation tutorial for UV-CDAT up to 2.4.0

UV-CDAT Build 101

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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other/uvcdat/installed.txt · Last modified: 2017/04/04 10:30 by jypeter