Difference between revisions of "Sep 19, 2018 - Installing software"
| (23 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
| − | Load modules | + | |
| + | == Load modules == | ||
| + | |||
| + | Add to <code>~/.bash_profile</code>: | ||
<source> | <source> | ||
| − | module load intel/intel-18 | + | module load intel/intel-18 |
module load intelmpi/2018.1.163 | module load intelmpi/2018.1.163 | ||
module load openmpi/3.0.0-intel-18 | module load openmpi/3.0.0-intel-18 | ||
module load gcc/7.3.0 | module load gcc/7.3.0 | ||
module load python/2.7.14 | module load python/2.7.14 | ||
| − | #necessary to have Intel MPI working | + | #necessary to have Intel MPI working on CITA cluster |
export I_MPI_FABRICS=shm:tcp | export I_MPI_FABRICS=shm:tcp | ||
export I_MPI_TCP_NETMASK=10.5.0.0 | export I_MPI_TCP_NETMASK=10.5.0.0 | ||
</source> | </source> | ||
| + | |||
| + | On Niagara, instead add | ||
| + | |||
| + | <source> | ||
| + | module load intel/2018.3 | ||
| + | module load python/3.6.4-anaconda5.1.0 | ||
| + | module load intelmpi/2018.3 | ||
| + | </source> | ||
| + | |||
| + | == Install FITSIO == | ||
| + | |||
| + | Download from [https://heasarc.gsfc.nasa.gov/fitsio/] | ||
| + | |||
| + | Run <code> ./configure </code> | ||
| + | |||
| + | Run <code> make </code> | ||
| + | |||
| + | == Install Healpix == | ||
| + | |||
| + | Download from [https://sourceforge.net/projects/healpix/] | ||
| + | |||
| + | Run <code>./configure</code> | ||
| + | |||
| + | Choose default choices unless otherwise stated. | ||
| + | |||
| + | Choose 3 (Fortran), ifort (F90 compiler), folder in which FITSIO was installed in the previous step (location of the cfitsio library). | ||
| + | |||
| + | Choose 4 (C++), 1 (basic_gcc configuration for C++ compilation) | ||
| + | |||
| + | Choose 5 (Python) [if using python 3, type "python3"] | ||
| + | |||
| + | Choose 0 (exit) | ||
| + | |||
| + | Add Healpix initialization to <code>~/.bash_profile</code> (see output after Fortran initialization). Source the file to reflect the changes. | ||
| + | |||
| + | Run <code>make</code> | ||
| + | |||
| + | Go for a coffee | ||
| + | |||
| + | P.S.: On Niagara, in the Fortran section of configure choose icc as the C compiler | ||
| + | |||
| + | == Install modified Lenspix == | ||
| + | |||
| + | Clone git repo <code>https://github.com/louis-pham/modified_lenspix</code> | ||
| + | |||
| + | Run <code>make</code> in <code>src</code> | ||
| + | |||
| + | As a test, run <code>python lens.py test_maps/kappa_map.fits test_maps/primary_alm.fits test_maps/phi_trial.fits test_maps/lensed_trial.fits -np 8</code> | ||
| + | |||
| + | Actually, on the first attempt the code started with <code>Creating zero map...</code>, then did a bunch of other things and then got stuck (or so it seemed). After termination and restarting all proceeded normally. | ||
| + | |||
| + | P.S.: On Niagara, it is necessary to replace all the | ||
| + | <code>print X</code> | ||
| + | by | ||
| + | <code>print(X)</code> | ||
| + | to be compliant with Python3 | ||
| + | |||
| + | We also had to perform following changes in Makefile: | ||
| + | * Add <code> cfitsio = /home/r/rbond/motloch/useful_software/cfitsio </code> | ||
| + | * Change the Fortran flags by editing cfitstio -L and adding curl to | ||
| + | <code> | ||
| + | F90FLAGS = $(FFLAGS) -I$(healpix) -I$(healpix)/include -L$(cfitsio) -L$(healpix)/lib $(LAPACKL) -lcfitsio -lcurl | ||
| + | </code> | ||
Latest revision as of 15:39, 7 May 2019
Load modules
Add to ~/.bash_profile:
module load intel/intel-18
module load intelmpi/2018.1.163
module load openmpi/3.0.0-intel-18
module load gcc/7.3.0
module load python/2.7.14
#necessary to have Intel MPI working on CITA cluster
export I_MPI_FABRICS=shm:tcp
export I_MPI_TCP_NETMASK=10.5.0.0On Niagara, instead add
module load intel/2018.3
module load python/3.6.4-anaconda5.1.0
module load intelmpi/2018.3Install FITSIO
Download from [1]
Run ./configure
Run make
Install Healpix
Download from [2]
Run ./configure
Choose default choices unless otherwise stated.
Choose 3 (Fortran), ifort (F90 compiler), folder in which FITSIO was installed in the previous step (location of the cfitsio library).
Choose 4 (C++), 1 (basic_gcc configuration for C++ compilation)
Choose 5 (Python) [if using python 3, type "python3"]
Choose 0 (exit)
Add Healpix initialization to ~/.bash_profile (see output after Fortran initialization). Source the file to reflect the changes.
Run make
Go for a coffee
P.S.: On Niagara, in the Fortran section of configure choose icc as the C compiler
Install modified Lenspix
Clone git repo https://github.com/louis-pham/modified_lenspix
Run make in src
As a test, run python lens.py test_maps/kappa_map.fits test_maps/primary_alm.fits test_maps/phi_trial.fits test_maps/lensed_trial.fits -np 8
Actually, on the first attempt the code started with Creating zero map..., then did a bunch of other things and then got stuck (or so it seemed). After termination and restarting all proceeded normally.
P.S.: On Niagara, it is necessary to replace all the
print X
by
print(X)
to be compliant with Python3
We also had to perform following changes in Makefile:
- Add
cfitsio = /home/r/rbond/motloch/useful_software/cfitsio - Change the Fortran flags by editing cfitstio -L and adding curl to
F90FLAGS = $(FFLAGS) -I$(healpix) -I$(healpix)/include -L$(cfitsio) -L$(healpix)/lib $(LAPACKL) -lcfitsio -lcurl