COSMOS is located in /usr/local/magellan/Cosmos2.
Before running any programs, you must execute the following commands:
The COSMOS software is installed on our software server, and should be usable from any local machine running CentOS 6.
Before running any programs, you must do the following:
source /data/software/Cosmos/Cosmos2-21/cosmos2-setupNOTE: Sourcing the cosmos2-setup file will now automatically set up your Perl environment also.
cd /home/joe/reductions/April_run/ cp $COSMOS_HOME/Cospar/* .NOTE: By default, COSMOS_PAR_DIR is set to ".", which means it expects the parameter files in your current directory (recommended). If you copy the entire Cospar directory over or copy the parameter files to a different directory, you will need to set the COSMOS_PAR_DIR environment variable to the full path of the directory that contains those parameter files you want to edit and use, e.g.:
cd /home/joe/reductions/April_run/ cp -r $COSMOS_HOME/Cospar /home/joe/reductions/ setenv COSMOS_PAR_DIR /home/joe/reductions/Cospar
task display8 = "/data/software/Cosmos/Cosmos2-21/bin/display8.cl"
The documentation is available locally at code.obs.carnegiescience.edu/cosmos
To download the latest source, click here.
COSMOS is known to work with the following:
Architecture | Operating System |
---|---|
x86 | Redhat 8, 9; Fedora Core 1, 4, 5; Mac OS X 10.4, 10.5 |
x86_64 | Fedora Core 8, Fedora 13, CentOS 6; Mac OS X 10.6, 10.7, 10.8, 10.9 |
PowerPC (G4, G5) | Mac OS X 10.3, 10.4 |
COSMOS should work on most other Linux systems, and may work on any UNIX variant.
COSMOS at this time does support FFTW3. There is a significant slow down in the way the code is runs with FFTW3. It is recommended to use the most recent version of FFTW2.
Please Note: On newer 64-bit operating systems, such as Fedora 13, Mac OS X 10.6, and Mac OS X 10.7, you have to be wary when building the PGPLOT Fortran libraries, in order to get the viewspectra program to work. In particular, the GIF, PPM, and WD driver files need to be edited.
Besides the usual stuff, you will need:
IMPORTANT NOTES (for Mac users): It's recommended that you use separate installations of the above dependencies, instead of using ones that are part of a package such as scisoft to prevent any compatibility issues. If you're running Mac OS X 10.6.x (Snow Leopard) or later, make sure you have both the 64-bit gcc and gfortran compilers for your system installed (download here) and that the location of their executables are at the front of your $PATH environment variable BEFORE installing these dependencies. |
mkdir /home/joe_user/COSMOS
tar -xzvf CosmosYYYY.tar.gz
setenv COSMOS_HOME "/home/joe_user/COSMOS/CosmosYYYY"
cd source
$COSMOS_HOME/lib
$COSMOS_HOME/lib
, (and $COSMOS_HOME/include
)
IMPORTANT (for Mac users): If you're running Mac OS X 10.6.x (Snow Leopard) or later, make sure you have both the 64-bit gcc and gfortran compilers for your system installed (download here) and that the location of their executables are at the front of your $PATH environment variable BEFORE running the following 'make' command. If you didn't install the 64-bit compilers by this point, see previous "IMPORTANT" note. |
make -f Makefile.system [PGLIB=pgplot-dir XLIB=Xll-dir FITSLIB=fits-dir PGINC=pgplot.h-dir XINC=X11.h-dir FITSINC=fits.h-dir]where system is either "Mac" or "linux", and the options in brackets are only needed if the above mentioned library and header files are not in their expected locations. With a little luck, you will get no error messages, and at the end you will have a completely installed system. If you encounter any errors, they are most likely due to a failure to find all the library and header files, in which case you should check their locations. If you're still having trouble, please refer to the FAQ page.
To compile ldss3-pattern:
$COSMOS_HOME/lib
$COSMOS_HOME/lib
, (and $COSMOS_HOME/include
)
make -f Makefile-ldss3.system [FITSLIB=fits-dir FFTWLIB=fftw-dir FITSINC=fits.h-dir FFTWINC=fftw.h-dir]Some final tidying:
setenv COSMOS_HOME "/home/joe-user/COSMOS/Cosmos2-21"
$COSMOS_HOME/Cospar
to the directory where you'll be reducing your data, or
$COSMOS_HOME/Cospar
directory to another location AND edit your cosmos2-setup file so that the COSMOS_PAR_DIR
environment variable points to that directory, e.g. if you copy it to /home/joe-user/reductions/Cospar, then you need to set the following:
setenv COSMOS_PAR_DIR "/home/joe-user/reductions/Cospar"
$COSMOS_HOME/Cospar
.
<module_name>.pm
), e.g.:
setenv PERLLIB "/home/joe_user/my-perl-modules-directory"If you are using COSMOS on a Mac, you may have Fink installed. If so, you may find a PERL5LIB environmental variable set, in which case you want to append PERLLIB to it by executing the following*:
setenv PERL5LIB "${PERLLIB}:${PERL5LIB}"If you are using COSMOS on Mac OS X 10.6 (Snow Leopard) booted in 32-bit mode, then you will also need to change the value of the environmental variable VERSIONER_PERL_PREFER_32_BIT by executing the following*:
setenv VERSIONER_PERL_PREFER_32_BIT no
COSMOS_HOME
, e.g.:
task display8 = "/home/joe_user/COSMOS/Cosmos2-21/bin/display8.cl"
source /home/joe-user/COSMOS/Cosmos2-21/cosmos2-setupYou can also put the above command in your shell startup file (e.g. ~/.cshrc) so that COSMOS can be used right away in every new terminal you open.
The HTML documentation will be available on your own computer at $COSMOS_HOME/docs/COSMOS.html
.