SeaDAS 7.5 RedHat varients now useless?

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oo_processing
Posts: 206
Joined: Wed Apr 06, 2005 12:11 pm America/New_York

SeaDAS 7.5 RedHat varients now useless?

by oo_processing » Sun May 13, 2018 2:28 pm America/New_York

Don,

It seems CentOS 6, not so much.
I installed a CentOS 6.9 virtual machine and a new version of cmake and git into a virtual CentOS6 machine.
NOTE THAT
$ gcc --version
gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-28)
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

And it is within the gcc-4.x  you specified.

This is where it errors out:

$ ./install_ocssw.py --install-dir=$INSTALL_DIR/ocssw --git-branch=v7.5 --src
Installing bundles.sha256sum (1 of 9)
--2018-05-13 14:09:17--  https://oceandata.sci.gsfc.nasa.gov/ocssw/bundles.sha256sum
Resolving oceandata.sci.gsfc.nasa.gov... xx.xxx.xx.xx, 2001:4d0:2418:128::84
Connecting to oceandata.sci.gsfc.nasa.gov|xx.xxx.xx.xx|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 3570 (3.5K) [application/octet-stream]
Saving to: “bundles.sha256sum”

100%[===================================================================================>] 3,570       --.-K/s   in 0s     

2018-05-13 14:09:18 (259 MB/s) - “bundles.sha256sum” saved [3570/3570]

Installing common (2 of 9)
Installing OCSSW_bash.env (3 of 9)
--2018-05-13 14:09:19--  https://oceandata.sci.gsfc.nasa.gov/ocssw/OCSSW_bash.env.v7.5
Resolving oceandata.sci.gsfc.nasa.gov... xx.xxx.xx.xx, 2001:4d0:2418:128::84
Connecting to oceandata.sci.gsfc.nasa.gov|xx.xxx.xx.xx|:443... connected.`GLIBC_2.14'
HTTP request sent, awaiting response... 200 OK
Length: 3001 (2.9K) [application/octet-stream]
Saving to: “OCSSW_bash.env.v7.5”

100%[===================================================================================>] 3,001       --.-K/s   in 0s     

2018-05-13 14:09:19 (210 MB/s) - “OCSSW_bash.env.v7.5” saved [3001/3001]

Installing ocrvc (4 of 9)
Installing bin (5 of 9)
Installing opt (6 of 9)
Installing src (7 of 9)
Installing opt-src (8 of 9)
--2018-05-13 14:09:23--  https://oceandata.sci.gsfc.nasa.gov/ocssw/opt-src-v7.5.tar
Resolving oceandata.sci.gsfc.nasa.gov... xx.xxx.xx.xx, 2001:4d0:2418:128::84
Connecting to oceandata.sci.gsfc.nasa.gov|xx.xxx.xx.xx|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 229611520 (219M) [application/octet-stream]
Saving to: “opt-src-v7.5.tar”

100%[===================================================================================>] 229,611,520 11.9M/s   in 17s    

2018-05-13 14:09:41 (12.6 MB/s) - “opt-src-v7.5.tar” saved [229611520/229611520]

Installing scripts (9 of 9)
hdp: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /home/bmurch/Programming/Seadas/Seadas-7.5/ocssw/opt/bin/../lib/libmfhdf.so.0)
hdp: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /home/bmurch/Programming/Seadas/Seadas-7.5/ocssw/opt/bin/../lib/libdf.so.0)
hdp: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /home/bmurch/Programming/Seadas/Seadas-7.5/ocssw/opt/bin/../lib/../lib/libxdr.so.0)
hdp: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /home/bmurch/Programming/Seadas/Seadas-7.5/ocssw/opt/bin/../lib/../lib/libjpeg.so.9)
Error - Can not run an installed executable

CentOS 6 has GLIBC_2.12, CentOS 7 has GLIBC_2.17 and thus works, is my guess.

Any ideas are appreciated as I must make this work on a Redhat 6 cluster. If those `GLIBC_2.14' compiled libs were compiled with GLIBC_2.12, I might stand a chance.

Thanks,
Brock

Tags:

OB SeaDAS - dshea
Subject Matter Expert
Subject Matter Expert
Posts: 214
Joined: Thu Mar 05, 2009 10:25 am America/New_York

SeaDAS 7.5 RedHat varients now useless?

by OB SeaDAS - dshea » Mon May 14, 2018 8:53 am America/New_York

- install CentOS 6 "Software Development Workstation"
- install cmake 3.11
    The binaries from cmake.org work fine.
- install a recent version of git > 2
- get newer compiler

$ yum install centos-release-scl
$ install devtoolset-4
$ scl enable devtoolset-4 bash

- get the source directories

$ install_ocssw.py -i ocssw -s
    script fails at the end running "hdp" as a sanity test, but src is installed

$ export OCSSWROOT=~/ocssw
$ source $OCSSWROOT/OCSSW_bash.env
$ cd $OCSSWROOT/opt
$ rm -rf EOS bin examples include lib share

- openjpg seemed to behave strangly, so need to fix it.
    edit $OCSSWROOT/opt/src/openjpeg/BuildIt
    add "-DBUILD_THIRDPARTY=ON" to the cmake line in the BuildIt script

- OK build the third party libs

$ cd $OCSSWROOT/opt/src
$ ./BuildIt

- some libs get stuffed into a lib64 directory.  Move them.

$ cd $OCSSWROOT/opt
$ mv lib64/* lib
$ mv lib64/cmake/* lib/cmake
$ mv lib64/pkgconfig/* lib/pkgconfig

- build OCSSW

$ cd $OCSSWROOT/ocssw-src
$ mkdir build
$ cd build
$ cmake ..
$ make -j 20 install

- this will get you everything except VIIRS.  I have a few ideas to
  make the old LIBC work.

oo_processing
Posts: 206
Joined: Wed Apr 06, 2005 12:11 pm America/New_York

SeaDAS 7.5 RedHat varients now useless?

by oo_processing » Mon May 14, 2018 12:30 pm America/New_York

I followed your directions to the letter from the virtual install of CentOS 6 "Software Development Workstation", and want to note the small difference in the install process:

#NOTE: the EOS and examples directories do not exist after running all_ocssw.py -i ocssw -s
#[bmurch@centos69 Seadas-7.5]$ cd /home/bmurch/Programming/Seadas/Seadas-7.5/ocssw/opt/
#[bmurch@centos69 opt]$ ll
#total 28
#drwxrwxr-x.  2 bmurch bmurch  4096 May 14 10:41 bin
#drwxrwxr-x.  7 bmurch bmurch  4096 May 14 10:41 include
#drwxrwxr-x.  4 bmurch bmurch 12288 May 14 10:41 lib
#drwxrwxr-x.  9 bmurch bmurch  4096 May 14 10:41 share
#drwxrwxr-x. 32 bmurch bmurch  4096 Mar 22 13:30 src\

Perhaps you had EOS and examples from before?

make -j 20 install finished without errors.

ALL THE ONES THAT HAVE VIIRS IN THE NAME FAIL AS EXPECTED.
# EG
[bmurch@centos69 build]$ /home/bmurch/Programming/Seadas/Seadas-7.5/ocssw/bin/l1aextract_viirs --help
/home/bmurch/Programming/Seadas/Seadas-7.5/ocssw/bin/l1aextract_viirs: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /home/bmurch/Programming/Seadas/Seadas-7.5/ocssw/bin/l1aextract_viirs)

# HOWEVER MANY OTHER BINARIES FAIL AS WELL. DID YOU TEST THE BINARIES BELOW? See:

[bmurch@centos69 build]$ l1agen_seawifs --help
l1agen_seawifs: /usr/lib64/libgfortran.so.3: version `GFORTRAN_1.4' not found (required by /home/bmurch/Programming/Seadas/Seadas-7.5/ocssw/bin/l1agen_seawifs)
/home/bmurch/Programming/Seadas/Seadas-7.5/ocssw/bin/l1agen_seawifs: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /home/bmurch/Programming/Seadas/Seadas-7.5/ocssw/bin/l1agen_seawifs)

[bmurch@centos69 bin]$ fixrgb
Segmentation fault (core dumped)

[bmurch@centos69 bin]$ interp_hycom_ascii
interp_hycom_ascii: error while loading shared libraries: libnetcdff.so.5: cannot open shared object file: No such file or directory

[bmurch@centos69 bin]$ l0cnst_read_modis
l0cnst_read_modis: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by l0cnst_read_modis)

[bmurch@centos69 bin]$ l0info_seawifs
l0info_seawifs: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by l0info_seawifs)

[bmurch@centos69 bin]$ l0regen_seawifs
l0regen_seawifs: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by l0regen_seawifs)

[bmurch@centos69 bin]$ l1agen_seawifs
l1agen_seawifs: /usr/lib64/libgfortran.so.3: version `GFORTRAN_1.4' not found (required by l1agen_seawifs)
l1agen_seawifs: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by l1agen_seawifs)

[bmurch@centos69 bin]$ l1info_aquarius
l1info_aquarius: error while loading shared libraries: libhdf5.so.10.1.0: cannot open shared object file: No such file or directory

[bmurch@centos69 bin]$ l2bin_aquarius
l2bin_aquarius: error while loading shared libraries: libnetcdf.so.7: cannot open shared object file: No such file or directory

[bmurch@centos69 bin]$ landbin
landbin: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by landbin)

[bmurch@centos69 bin]$ landtimebin
landtimebin: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by landtimebin)

[bmurch@centos69 bin]$ mk_aquarius_ancillary_data
mk_aquarius_ancillary_data: error while loading shared libraries: libhdf5_fortran.so.10.1.0: cannot open shared object file: No such file or directory

[bmurch@centos69 bin]$ oisst_info
oisst_info: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by oisst_info)

[bmurch@centos69 bin]$ smigen
smigen: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by smigen)

[bmurch@centos69 bin]$ solar_xray
solar_xray: error while loading shared libraries: libhdf5.so.10.1.0: cannot open shared object file: No such file or directory

[bmurch@centos69 bin]$ swh
swh: error while loading shared libraries: libhdf5.so.10.1.0: cannot open shared object file: No such file or directory

[bmurch@centos69 bin]$ tec
tec: error while loading shared libraries: libhdf5.so.10.1.0: cannot open shared object file: No such file or directory

OB.DAAC - SeanBailey
User Services
User Services
Posts: 1167
Joined: Wed Sep 18, 2019 6:15 pm America/New_York

SeaDAS 7.5 RedHat varients now useless?

by OB.DAAC - SeanBailey » Mon May 14, 2018 2:40 pm America/New_York

Those binaries are not build by default, so unless you modified your CMake configuration to include building them, you've still got the binaries we distributed.
BTW, you very likely don't need any of them anyway, so probably not worth your effort to rebuild them.

But so you'll believe me:

l1agen_seawifs is used to generate a SeaWiFS L1A file from a L0 file.  SeaWiFS is dead....no more L0 data coming down.
Similary vestigial are l0info_seawifs and l0regen_seawifs.

fixrgb is so unnecessary not worth mentioning, but so you don't feel the need to ask - SeaWiFS True Color browse images could sometimes have pink or blue stripes with bad input data - this "fixed" those.

l0cnst_read_modis - just not needed, unless you REALLY want to read a MODIS L0 constructor file...trust me, you don't care.
The same is true of oisst_info (but for OISST files)

These: l1info_aquarius, l2bin_aquarius, mk_aquarius_ancillary_data, solar_xray, swh, tec, and interp_hycom_ascii
are all for Aquarius processing (both data and ancillary generation - something I really doubt you have a need to do.) 

landbin and landtimebin are dead wood from the wayback machine of SeaWiFS Land processing.  Both are superseded by l2bin/l3bin/l3mapgen now

smigen - replaced by l3mapgen

Long story short - there are a LOT of things we have or had programs for that are not terribly useful to the SeaDAS user community - these you can ignore

Sean

treble
Posts: 20
Joined: Thu Jan 24, 2008 1:33 pm America/New_York

SeaDAS 7.5 RedHat varients now useless?

by treble » Mon May 14, 2018 6:59 pm America/New_York

I installed SeaDAS on my CentOS 7 server with glibc 2.17 as:
./install_ocssw.py --install-dir=./ocssw --git-branch=v7.5 --aqua --seawifs
then removed $OCSSWROOT/opt/lib/libquadmath.so.0 as Sean suggested and it seems to be working!  So no need to compile from source!  (only tested l3mapgen and l2gen).
Thanks Sean!

oo_processing
Posts: 206
Joined: Wed Apr 06, 2005 12:11 pm America/New_York

SeaDAS 7.5 RedHat varients now useless?

by oo_processing » Wed May 16, 2018 3:33 pm America/New_York

Don,

I am trying to get the code to install on my RHEL 6 cluster. It builds fine, but when I do the make -j 20 install it fails. See below on VIIRS:

[bmurch@optics0 build]$ gcc --version
gcc (GCC) 4.9.4
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
[bmurch@optics0 build]$ cmake --version
cmake version 3.7.1
CMake suite maintained and supported by Kitware (kitware.com/cmake).

$ install_ocssw.py -i ocssw -s
    script fails at the end running "hdp" as a sanity test, but src is installed

$ export OCSSWROOT=~/ocssw
$ source $OCSSWROOT/OCSSW_bash.env
$ cd $OCSSWROOT/opt
$ rm -rf EOS bin examples include lib share

- openjpg seemed to behave strangly, so need to fix it.
    edit $OCSSWROOT/opt/src/openjpeg/BuildIt
    add "-DBUILD_THIRDPARTY=ON" to the cmake line in the BuildIt script

From:
https://oceancolor.gsfc.nasa.gov/forum/oceancolor/topic_show.pl?pid=37368#pid37368

    edit ocssw/ocssw-src/CMakeLists.txt line 29
    OPTION(BUILD_VIIRS_L1 "Build VIIRS L1 code" ON)
  grep "Build VIIRS L1 code" $OCSSWROOT/ocssw-src/CMakeLists.txt
  OPTION(BUILD_VIIRS_L1 "Build VIIRS L1 code" ON)

- OK build the third party libs

$ cd $OCSSWROOT/opt/src
$ ./BuildIt

- some libs get stuffed into a lib64 directory.  Move them.

$ cd $OCSSWROOT/opt
$ mv lib64/* libll $OCC
$ mv lib64/cmake/* lib/cmake
$ mv lib64/pkgconfig/* lib/pkgconfig

- build OCSSW

$ cd $OCSSWROOT/ocssw-src
$ mkdir build
$ cd build
$ cmake ..
$ make -j 20 install

goes though everything until I get to the make.
which seems to FAIL as it cannot find the viirs directories even with the OPTION(BUILD_VIIRS_L1 "Build VIIRS L1 code" ON)  in the ocssw/ocssw-src/CMakeLists.txt file. Errors here:

make[2]: *** [src/l2gen/CMakeFiles/l1brsgen.dir/l1_viirs_nc.c.o] Error 1
make[2]: *** Waiting for unfinished jobs....
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
make[1]: *** [src/l2gen/CMakeFiles/l1brsgen.dir/all] Error 2
make: *** [all] Error 2
[ 33%] Linking Fortran executable l2bin
...
[ 33%] Building C object src/l2gen/CMakeFiles/l1bgen_generic.dir/l1_mos_hdf.c.o
/shares/cms_optics/apps/seadas/ocssw/ocssw-src/src/l2gen/l1_viirs_nc.c:12:39: fatal error: Calibrate_Viirs_Connector.h: No such file or directory
#include <Calibrate_Viirs_Connector.h>
                                       ^
compilation terminated.
make[2]: *** [src/l2gen/CMakeFiles/lonlat2pixline.dir/l1_viirs_nc.c.o] Error 1
make[2]: *** Waiting for unfinished jobs....
...
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 34%] Building C object src/l2gen/CMakeFiles/l1info.dir/l1_ocm2_hdf.c.o
...
[ 36%] Building C object src/l2gen/CMakeFiles/l1info.dir/l1b_viirs_nc.c.o
/shares/cms_optics/apps/seadas/ocssw/ocssw-src/src/l2gen/l1_viirs_nc.c:12:39: fatal error: Calibrate_Viirs_Connector.h: No such file or directory
#include <Calibrate_Viirs_Connector.h>
                                       ^
compilation terminated.
make[2]: *** [src/l2gen/CMakeFiles/l1bgen_generic.dir/l1_viirs_nc.c.o] Error 1
make[2]: *** Waiting for unfinished jobs....
[ 36%] Building C object src/l2gen/CMakeFiles/l1info.dir/l1_viirs_nc.c.o
...
[ 36%] Linking CXX static library libbin++.a
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 36%] Linking CXX executable l3bin64
...
[ 36%] Building Fortran object src/l2gen/CMakeFiles/l1info.dir/lenstr.f.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 36%] Building Fortran object src/l2gen/CMakeFiles/l1info.dir/raygetpol.f.o
[ 36%] Built target l3bin64
[ 37%] Building Fortran object src/l2gen/CMakeFiles/l1info.dir/simpsn.f.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 37%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/xcal.c.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 37%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/get_f0.c.o
...
[ 37%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/atmocor1_land.c.o
/shares/cms_optics/apps/seadas/ocssw/ocssw-src/src/l2gen/l1_viirs_nc.c:12:39: fatal error: Calibrate_Viirs_Connector.h: No such file or directory
#include <Calibrate_Viirs_Connector.h>
                                       ^
compilation terminated.
make[2]: *** [src/l2gen/CMakeFiles/l1info.dir/l1_viirs_nc.c.o] Error 1
make[2]: *** Waiting for unfinished jobs....
[ 37%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/whitecaps.c.o
...
[ 37%] Building C object src/l2gen/CMakeFiles/l1mapgen.dir/l1_octs_hdf.c.o
make[2]: *** No rule to make target `/shares/cms_optics/apps/seadas/ocssw/opt/lib/libViirsCal.a', needed by `src/l2gen/l2binmatch64'.  Stop.
make[2]: *** Waiting for unfinished jobs....
[ 37%] Building C object src/l2gen/CMakeFiles/l2binmatch64.dir/elev.c.o
[ 37%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/b128_box_num.c.o
[ 37%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/read_mask.c.o
[ 37%] Building C object src/l2gen/CMakeFiles/l1mapgen.dir/l1_czcs_hdf.c.o
make[1]: *** [src/l2gen/CMakeFiles/l1info.dir/all] Error 2
[ 37%] Building C object src/l2gen/CMakeFiles/l1mapgen.dir/ll2vec.c.o
...
[ 38%] Building Fortran object src/l2gen/CMakeFiles/l1mapgen.dir/raygetpol.f.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 38%] Building Fortran object src/l2gen/CMakeFiles/l1mapgen.dir/simpsn.f.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
make[1]: *** [src/l2gen/CMakeFiles/l2binmatch64.dir/all] Error 2
[ 38%] Building Fortran object src/l2gen/CMakeFiles/l1mapgen.dir/airmass_avhrr.f.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 38%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/l1_hdf_generic_read.c.o
[ 38%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/l1_nc_generic_read.c.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 38%] Building Fortran object src/l2gen/CMakeFiles/l1mapgen.dir/avhrrsub5h.f.o
[ 38%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/l1_generic_write.c.o
/shares/cms_optics/apps/seadas/ocssw/ocssw-src/src/l2gen/l1_viirs_nc.c:12:39: fatal error: Calibrate_Viirs_Connector.h: No such file or directory
#include <Calibrate_Viirs_Connector.h>
                                       ^
compilation terminated.
make[2]: *** [src/l2gen/CMakeFiles/l1mapgen.dir/l1_viirs_nc.c.o] Error 1
make[2]: *** Waiting for unfinished jobs....
[ 38%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/l1_mos_hdf.c.o
[ 38%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/l1_octs_hdf.c.o
[ 38%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/l1_czcs_hdf.c.o
[ 39%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/ll2vec.c.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 39%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/l1a_seawifs.c.o
[ 39%] Building Fortran object src/l2gen/CMakeFiles/l1brsgen.dir/etbpsub.f.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 39%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/ftrim.c.o
[ 39%] Building Fortran object src/l2gen/CMakeFiles/l1brsgen.dir/hmf8.f.o
make[1]: *** [src/l2gen/CMakeFiles/l1mapgen.dir/all] Error 2
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 39%] Building Fortran object src/l2gen/CMakeFiles/l1brsgen.dir/lenstr.f.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 39%] Building Fortran object src/l2gen/CMakeFiles/l1brsgen.dir/raygetpol.f.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 39%] Building Fortran object src/l2gen/CMakeFiles/l1brsgen.dir/simpsn.f.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 39%] Building Fortran object src/l2gen/CMakeFiles/l1brsgen.dir/airmass_avhrr.f.o
/shares/cms_optics/apps/seadas/ocssw/ocssw-src/src/l2gen/l1_viirs_nc.c:12:39: fatal error: Calibrate_Viirs_Connector.h: No such file or directory
#include <Calibrate_Viirs_Connector.h>
                                       ^
compilation terminated.
make[2]: *** [src/l2gen/CMakeFiles/l1brsgen.dir/l1_viirs_nc.c.o] Error 1
make[2]: *** Waiting for unfinished jobs....
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
make[1]: *** [src/l2gen/CMakeFiles/l1brsgen.dir/all] Error 2
make: *** [all] Error 2

oo_processing
Posts: 206
Joined: Wed Apr 06, 2005 12:11 pm America/New_York

SeaDAS 7.5 RedHat varients now useless?

by oo_processing » Wed May 16, 2018 4:28 pm America/New_York

Don,

I am trying to get the code to install on my RHEL 6 cluster. It builds fine, but when I do the "make -j 20 install" it fails. SEE PART I.
"SEE PART II" very bottom below for errors when instructions followed exclude the OPTION(BUILD_VIIRS_L1 "Build VIIRS L1 code" ON)

PART I
[bmurch@optics0 build]$ gcc --version
gcc (GCC) 4.9.4
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
[bmurch@optics0 build]$ cmake --version
cmake version 3.7.1
CMake suite maintained and supported by Kitware (kitware.com/cmake).

$ install_ocssw.py -i ocssw -s
    script fails at the end running "hdp" as a sanity test, but src is installed

$ export OCSSWROOT=~/ocssw
$ source $OCSSWROOT/OCSSW_bash.env
$ cd $OCSSWROOT/opt
$ rm -rf EOS bin examples include lib share

- openjpg seemed to behave strangly, so need to fix it.
    edit $OCSSWROOT/opt/src/openjpeg/BuildIt
    add "-DBUILD_THIRDPARTY=ON" to the cmake line in the BuildIt script

From:
https://oceancolor.gsfc.nasa.gov/forum/oceancolor/topic_show.pl?pid=37368#pid37368

    edit ocssw/ocssw-src/CMakeLists.txt line 29
    OPTION(BUILD_VIIRS_L1 "Build VIIRS L1 code" ON)
  grep "Build VIIRS L1 code" $OCSSWROOT/ocssw-src/CMakeLists.txt
  OPTION(BUILD_VIIRS_L1 "Build VIIRS L1 code" ON)

- OK build the third party libs

$ cd $OCSSWROOT/opt/src
$ ./BuildIt

- some libs get stuffed into a lib64 directory.  Move them.

$ cd $OCSSWROOT/opt
$ mv lib64/* libll $OCC
$ mv lib64/cmake/* lib/cmake
$ mv lib64/pkgconfig/* lib/pkgconfig

- build OCSSW

$ cd $OCSSWROOT/ocssw-src
$ mkdir build
$ cd build
$ cmake ..
$ make -j 20 install

goes though everything until I get to the make.
which seems to FAIL as it cannot find the viirs directories even with the OPTION(BUILD_VIIRS_L1 "Build VIIRS L1 code" ON)  in the ocssw/ocssw-src/CMakeLists.txt file. Errors here:

make[2]: *** [src/l2gen/CMakeFiles/l1brsgen.dir/l1_viirs_nc.c.o] Error 1
make[2]: *** Waiting for unfinished jobs....
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
make[1]: *** [src/l2gen/CMakeFiles/l1brsgen.dir/all] Error 2
make: *** [all] Error 2
[ 33%] Linking Fortran executable l2bin
...
[ 33%] Building C object src/l2gen/CMakeFiles/l1bgen_generic.dir/l1_mos_hdf.c.o
/shares/cms_optics/apps/seadas/ocssw/ocssw-src/src/l2gen/l1_viirs_nc.c:12:39: fatal error: Calibrate_Viirs_Connector.h: No such file or directory
#include <Calibrate_Viirs_Connector.h>
                                       ^
compilation terminated.
make[2]: *** [src/l2gen/CMakeFiles/lonlat2pixline.dir/l1_viirs_nc.c.o] Error 1
make[2]: *** Waiting for unfinished jobs....
...
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 34%] Building C object src/l2gen/CMakeFiles/l1info.dir/l1_ocm2_hdf.c.o
...
[ 36%] Building C object src/l2gen/CMakeFiles/l1info.dir/l1b_viirs_nc.c.o
/shares/cms_optics/apps/seadas/ocssw/ocssw-src/src/l2gen/l1_viirs_nc.c:12:39: fatal error: Calibrate_Viirs_Connector.h: No such file or directory
#include <Calibrate_Viirs_Connector.h>
                                       ^
compilation terminated.
make[2]: *** [src/l2gen/CMakeFiles/l1bgen_generic.dir/l1_viirs_nc.c.o] Error 1
make[2]: *** Waiting for unfinished jobs....
[ 36%] Building C object src/l2gen/CMakeFiles/l1info.dir/l1_viirs_nc.c.o
...
[ 36%] Linking CXX static library libbin++.a
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 36%] Linking CXX executable l3bin64
...
[ 36%] Building Fortran object src/l2gen/CMakeFiles/l1info.dir/lenstr.f.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 36%] Building Fortran object src/l2gen/CMakeFiles/l1info.dir/raygetpol.f.o
[ 36%] Built target l3bin64
[ 37%] Building Fortran object src/l2gen/CMakeFiles/l1info.dir/simpsn.f.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 37%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/xcal.c.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 37%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/get_f0.c.o
...
[ 37%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/atmocor1_land.c.o
/shares/cms_optics/apps/seadas/ocssw/ocssw-src/src/l2gen/l1_viirs_nc.c:12:39: fatal error: Calibrate_Viirs_Connector.h: No such file or directory
#include <Calibrate_Viirs_Connector.h>
                                       ^
compilation terminated.
make[2]: *** [src/l2gen/CMakeFiles/l1info.dir/l1_viirs_nc.c.o] Error 1
make[2]: *** Waiting for unfinished jobs....
[ 37%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/whitecaps.c.o
...
[ 37%] Building C object src/l2gen/CMakeFiles/l1mapgen.dir/l1_octs_hdf.c.o
make[2]: *** No rule to make target `/shares/cms_optics/apps/seadas/ocssw/opt/lib/libViirsCal.a', needed by `src/l2gen/l2binmatch64'.  Stop.
make[2]: *** Waiting for unfinished jobs....
[ 37%] Building C object src/l2gen/CMakeFiles/l2binmatch64.dir/elev.c.o
[ 37%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/b128_box_num.c.o
[ 37%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/read_mask.c.o
[ 37%] Building C object src/l2gen/CMakeFiles/l1mapgen.dir/l1_czcs_hdf.c.o
make[1]: *** [src/l2gen/CMakeFiles/l1info.dir/all] Error 2
[ 37%] Building C object src/l2gen/CMakeFiles/l1mapgen.dir/ll2vec.c.o
...
[ 38%] Building Fortran object src/l2gen/CMakeFiles/l1mapgen.dir/raygetpol.f.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 38%] Building Fortran object src/l2gen/CMakeFiles/l1mapgen.dir/simpsn.f.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
make[1]: *** [src/l2gen/CMakeFiles/l2binmatch64.dir/all] Error 2
[ 38%] Building Fortran object src/l2gen/CMakeFiles/l1mapgen.dir/airmass_avhrr.f.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 38%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/l1_hdf_generic_read.c.o
[ 38%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/l1_nc_generic_read.c.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 38%] Building Fortran object src/l2gen/CMakeFiles/l1mapgen.dir/avhrrsub5h.f.o
[ 38%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/l1_generic_write.c.o
/shares/cms_optics/apps/seadas/ocssw/ocssw-src/src/l2gen/l1_viirs_nc.c:12:39: fatal error: Calibrate_Viirs_Connector.h: No such file or directory
#include <Calibrate_Viirs_Connector.h>
                                       ^
compilation terminated.
make[2]: *** [src/l2gen/CMakeFiles/l1mapgen.dir/l1_viirs_nc.c.o] Error 1
make[2]: *** Waiting for unfinished jobs....
[ 38%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/l1_mos_hdf.c.o
[ 38%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/l1_octs_hdf.c.o
[ 38%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/l1_czcs_hdf.c.o
[ 39%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/ll2vec.c.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 39%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/l1a_seawifs.c.o
[ 39%] Building Fortran object src/l2gen/CMakeFiles/l1brsgen.dir/etbpsub.f.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 39%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/ftrim.c.o
[ 39%] Building Fortran object src/l2gen/CMakeFiles/l1brsgen.dir/hmf8.f.o
make[1]: *** [src/l2gen/CMakeFiles/l1mapgen.dir/all] Error 2
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 39%] Building Fortran object src/l2gen/CMakeFiles/l1brsgen.dir/lenstr.f.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 39%] Building Fortran object src/l2gen/CMakeFiles/l1brsgen.dir/raygetpol.f.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 39%] Building Fortran object src/l2gen/CMakeFiles/l1brsgen.dir/simpsn.f.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 39%] Building Fortran object src/l2gen/CMakeFiles/l1brsgen.dir/airmass_avhrr.f.o
/shares/cms_optics/apps/seadas/ocssw/ocssw-src/src/l2gen/l1_viirs_nc.c:12:39: fatal error: Calibrate_Viirs_Connector.h: No such file or directory
#include <Calibrate_Viirs_Connector.h>
                                       ^
compilation terminated.
make[2]: *** [src/l2gen/CMakeFiles/l1brsgen.dir/l1_viirs_nc.c.o] Error 1
make[2]: *** Waiting for unfinished jobs....
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
make[1]: *** [src/l2gen/CMakeFiles/l1brsgen.dir/all] Error 2
make: *** [all] Error 2

PART II
When I try it without making this change:
edit ocssw/ocssw-src/CMakeLists.txt line 29
    OPTION(BUILD_VIIRS_L1 "Build VIIRS L1 code" ON)

It builds fine, and the "$ make -j 20 install" install works fine.
BUT, only one viirs binary seems to work.

[bmurch@optics0 bin]$ ls *viirs*
calibrate_viirs  geolocate_viirs  l1aextract_viirs  l2bin_viirs  viirs_obc
[bmurch@optics0 bin]$ calibrate_viirs
calibrate_viirs: /lib64/libc.so.6: version `GLIBC_2.17' not found (required by calibrate_viirs)
calibrate_viirs: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by calibrate_viirs)
[bmurch@optics0 bin]$ geolocate_viirs
geolocate_viirs: /lib64/libc.so.6: version `GLIBC_2.17' not found (required by geolocate_viirs)
geolocate_viirs: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by geolocate_viirs)
[bmurch@optics0 bin]$ l1aextract_viirs
l1aextract_viirs: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by l1aextract_viirs)
[bmurch@optics0 bin]$ viirs_obc
viirs_obc: /lib64/libc.so.6: version `GLIBC_2.17' not found (required by viirs_obc)
viirs_obc: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by viirs_obc)
[bmurch@optics0 bin]$ l2bin_viirs
L2BIN_VIIRS 2.2.13 (May 18 2015 09:12:42)
This is version 2.2.13 of l2bin_viirs (compiled on May 18 2015 09:12:42)

Usage: l2bin_viirs parfile=parfile or
            infile=infile ofile=ofile [sday=sday] [eday=eday]
            resolve=resolve [flaguse=flaguse] [l3bprod=l3bprod]
            [prodtype=prodtype] [noext=noext]
            [rowgroup=rowgroup] [night=night]

   parfile   = parameter filename
   infile    = input filename/filelist
   ofile     = output bin filename
   sday      = start datadate (YYYYDDD) [ignored for "regional" prodtype]
   eday      = end datadate   (YYYYDDD) [ignored for "regional" prodtype]
   resolve   = bin resolution (H,1,2,4,9,36)
   flaguse   = flags masked [see /SENSOR/l2bin_defaults.par]
   l3bprod   = bin products [default=all products]
               Set to "ALL" or "all" for all L2 products in 1st input file.
               Use ':' or ',' or ' ' as delimiters.
               Use ';' or '=' to delineate minimum values.
   prodtype  = product type (Set to "regional" to bin all scans.) [default=day]
   noext     = set to 1 to suppress generation of external files
               [default=0, (1 for "regional" prodtype)]
   rowgroup  = # of bin rows to process at once.
   night     = set to 1 for SST night processing [default=0]
   qual_max  = maximum acceptable quality [default=2]
   verbose   = Allow more verbose screen messages [default=0]

nrl7331
Posts: 2
Joined: Wed Apr 18, 2018 10:26 am America/New_York

SeaDAS 7.5 RedHat varients now useless?

by nrl7331 » Wed May 16, 2018 6:36 pm America/New_York

Actually, Sean, one of my issues was with libquadmath.so.
To compile on SL7.3, I went to opt and mv lib lib.save, mv bin bin.save (as you'll need this later!).
Then I rebuilt the 3rd party stuff.  Only issue I had was that puixml, liblapack, ..., which installed in a 'lib64' instead of 'lib'.  So, I just moved them.
Then in opt/lib, you need copy the libViirs*a static libraries since the code to build them does not exist.  Also libnovas.a.
Once I had the 3rd party stuff recompiled, I was able to rebuild OCSSW  (mkdir build, cd build, cmake .., make).  I had two minor fixes that Sean has evidently pushed.
Paul

OB SeaDAS - dshea
Subject Matter Expert
Subject Matter Expert
Posts: 214
Joined: Thu Mar 05, 2009 10:25 am America/New_York

SeaDAS 7.5 RedHat varients now useless?

by OB SeaDAS - dshea » Fri May 18, 2018 2:10 pm America/New_York

I put up a new web page with a link to the VIIRS libs you need to compile on CentOS 6.
This page also describs running and compiling on CentOS 7

https://seadas.gsfc.nasa.gov/build_ocssw/rhel/

don

oo_processing
Posts: 206
Joined: Wed Apr 06, 2005 12:11 pm America/New_York

SeaDAS 7.5 RedHat varients now useless?

by oo_processing » Fri May 18, 2018 8:02 pm America/New_York

Don

Thanks so much. :grin::grin::grin:
I was able to compile with the viirs tar.
However, not having done this before with OCSSW, I suspect I'm missing something.

When I tried this:
geolocate_viirs v ifile=V2018137192400.L1A_SNPP.nc geofile_mod=V20181371942.GEO
it came back with an error:  "Can't open parameter file - $OCSSWROOT/share/viirs/npp/instrument_default"

Then I remembered the DEM files too, so I grabbed them and when I tried to install them, I noticed that there was no $OCSSWROOT/share/viirs directory.

So I thought I needed to "install_opcssw.py --viirs" and it went and git everything (Bundles 1 - 10) failing on 9. Is there some way to exclude some of these bundles? I modify the OCSSW_bash.env, and it is overwritten every time (as well as modifications to other files eg: HiRES=1) are overwritten. Does this flag function in that way: --no-update

"geolocate_viirs v ifile=V2018137192400.L1A_SNPP.nc geofile_mod=V20181371942.GEO" now returns all the GLIBC 2.14/17 symbol errors
Alas, what am I missing? I usually use the GUI to install the individuals like MODIST, MODISA,  OLCI .... Obviously that won't work.

Should I be installing everything (all sensors) first (to get all the proper directories and files) and then install the source, and then follow the directions https://seadas.gsfc.nasa.gov/build_ocssw/rhel/ again?

Or something like this:
./install_ocssw.py -v -c --src  --aquarius --avhrr --czcs  --goci  --hico --meris --aqua --terra  --mos  --msi  --ocm1  --ocm2 --octs --olcis3a --oli --osmi --seawifs --viirsn --viirsj1

And then the CentOS6 source build?

And most importantly, what should I be doing in the future so that I don't mess things up with a git of files that are not good for the CentOS6 boxes?

Thanks,
Brock

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