- FAQ: How to switch Cocoa's adopted CAMB/CLASS? (the easy way)
- FAQ: What about installing Polychord and Velocileptors?
- FAQ: How to download and compile likelihoods for modern CMB data?
- FAQ: How to switch the default CAMB/CLASS? (the not-so-easy way)
- FAQ: How to add additional patches to the default CAMB/CLASS?
- Understanding CAMB's patches
- Understanding CLASS's patches
Installing a new CAMB code in Cocoa requires a few changes to the existing CAMB/CLASS code. Fortunately, Cocoa provides a set of scripts, located at Cocoa/installation_scripts, and patches, located at Cocoa/../cocoa_installation_libraries/XXX_changes where XXX is the specific code to be patched, that automatically handle the necessary code adjustments.
The shell scripts are split into two categories. The first category of shell scripts downloads the code and applies necessary patches; they are named setup_XXX.sh, where XXX is the specific code to be downloaded. For instance, the script setup_camb.sh downloads CAMB Boltzmann code from its original GitHub repository. The second category of shell scripts compiles the code; they are named compile_XXX.sh. For instance, the script setup_camb.sh compiles CAMB.
The patches are always located at Cocoa/../cocoa_installation_libraries. These patches enforce that these codes are compiled with the Cocoa-prescribed compilers and linked against the Cocoa-prescribed version of any necessary numerical library. Consistency when compiling and linking code is one of the main advantages of working within the Cocoa framework.
On an advanced note, three scripts are worth mentioning separately: setup_core_packages.sh, unxv_core_packages.sh, and compile_core_packages.sh. The first two scripts manage the installation, while the third manages the compilation of stable numerical libraries that other codes may need. The vast majority of these codes are provided by the Cocoa Conda environment, with a few exceptions, including the CUBA integration library. Nevertheless, these scripts provide a unified and simple interface for users to add new required numerical libraries that may not be available on Conda (or that need some unique way to be compiled).
Swapping the default CAMB/CLASS is simple. Go to Cocoa's main folder and open the file set_installation_options.sh. Then, adjust the following environmental keys.
[Adapted from Cocoa/set_installation_options.sh shell script]
export CAMB_URL="https://github.com/cmbant/CAMB"
export CAMB_GIT_COMMIT="45d1c3d27e7480c0f9a82c98522c17ed422dd408"
export CAMB_NAME='CAMB'
export CLASS_URL="https://github.com/lesgourg/class_public.git"
export CLASS_GIT_COMMIT="8df566c1ff2d0b3e40e106567c435575aea337be"
export CLASS_NAME="class_public"
As long as your new CAMB/CLASS makefiles are not altered to the extent that Cocoa patch files designed to adjust CAMB installation and CLASS installation fail, that is all that is needed to change the adopted Boltzmann codes.
What happens if the Cocoa patch files fail? We have three sections dedicated to this problem. Check FAQ: How to add additional patches to the default CAMB/CLASS?, and Understanding CAMB's patches, and Understanding CLASS's patches.
Finally, what if the user wants to skip CAMB or CLASS compilation? In this case, the shell script Cocoa/set_installation_options.sh provides the following environmental keys.
[Adapted from Cocoa/set_installation_options.sh shell script]
#export IGNORE_CAMB_CODE=1
#export IGNORE_CLASS_CODE=1
The shell script set_installation_options.sh provides the following keys that manage the download and compilation of Polychord and Velocileptor.
[Adapted from Cocoa/set_installation_options.sh shell script]
#export IGNORE_POLYCHORD_SAMPLER_CODE=1
#export IGNORE_VELOCILEPTORS_CODE=1
(...)
export POLY_URL="https://github.com/PolyChord/PolyChordLite.git"
export POLYCHORD_GIT_COMMIT="daba49d1385d065122db76a2b384050f9e95d278"
export POLY_NAME="PolyChordLite"
(...)
export VELOCILEPTORS_URL="https://github.com/sfschen/velocileptors.git"
export VELOCILEPTORS_GIT_COMMIT="889a0c98895831eb23b250a26162cfb8a93237bd"
export VELOCILEPTORS_NAME="velocileptors"
The CMB data sets require specialized likelihoods. Cocoa will download, patch, and compile them as long as these following keys are not set on Cocoa/set_installation_options.sh
[Adapted from Cocoa/set_installation_options.sh shell script]
# ------------------------------------------------------------------------------
# The keys below control which packages will be installed and compiled when ----
# running setup_cocoa.sh and compile_cocoa.sh. They are mostly helpful when ----
# debugging cocoa --------------------------------------------------------------
# ------------------------------------------------------------------------------
(...)
#export IGNORE_PLANCK_LIKELIHOOD_CODE=1
#export IGNORE_ACTDR4_CODE=1
#export IGNORE_ACTDR6_CODE=1
#export IGNORE_SIMONS_OBSERVATORY_LIKELIHOOD_CODE=1
#export IGNORE_CAMSPEC_LIKELIHOOD_CODE=1
#export IGNORE_LIPOP_LIKELIHOOD_CODE=1
Cocoa selects the URL to download the likelihoods (and the version of the likelihood) using the following keys.
[Adapted from Cocoa/set_installation_options.sh shell script]
# ------------------------------------------------------------------------------
# PACKAGE URL AND VERSIONS. CHANGES IN THE COMMIT ID MAY BREAK COCOA -----------
# ------------------------------------------------------------------------------
(...)
export HILLIPOP_URL="https://github.com/planck-npipe/hillipop.git"
export HILLIPOP_GIT_COMMIT="cc9cbe31991d4662522241543a46d44d2cdec251"
export LOLLIPOP_URL="https://github.com/planck-npipe/lollipop.git"
export LOLLIPOP_GIT_COMMIT="280a9c93d33bc6a058d6bf769ec82d9f7fdbd2b6"
If users want to create their setup and compile shell scripts to work seamlessly with multiple modified Boltzmann codes, they must follow the steps below. Here, we assume the users want to create a new modified CAMB named CAMBQ (the modified class case is similar).
Step 1️⃣: Copy the setup and compile shell scripts.
cp "${ROOTDIR:?}"/installation_scripts/setup_camb "${ROOTDIR:?}"/installation_scripts/setup_cambq
and
cp "${ROOTDIR:?}"/installation_scripts/compile_camb "${ROOTDIR:?}"/installation_scripts/compile_cambq
Step 2️⃣: Modify the name of the environmental variables CAMB_URL, CAMB_NAME, and CAMB_GIT_COMMIT on setup_cambq.sh shell script.
[Adapted from Cocoa/installation_scripts/setup_cambq.sh shell script]
CCIL="${ROOTDIR:?}/../cocoa_installation_libraries"
(...)
#URL="${CAMB_URL:-"https://github.com/cmbant/CAMB"}" # Original line - commented
URL="${CAMBQ_URL:-"https://github.com/CAMBQ"}"
(...)
# If the default patches work on the modified CAMBQ, there is no need to modify the line below
#CHANGES="${CCIL:?}/camb_changes" # Original line - commented
CHANGES="${CCIL:?}/cambq_changes"
#FOLDER="${CAMB_NAME:-"CAMB"}" # Original line - commented
FOLDER="${CAMBQ_NAME:-"CAMBQ"}"
(...)
#if [ -n "${CAMB_GIT_COMMIT}" ]; then # Original line - commented
# "${GIT:?}" checkout "${CAMB_GIT_COMMIT:?}" \ # Original line - commented
if [ -n "${CAMBQ_GIT_COMMIT}" ]; then
"${GIT:?}" checkout "${CAMBQ_GIT_COMMIT:?}" \
>${OUT1:?} 2>${OUT2:?} || { error "${EC16:?}"; return 1; }
fi
Step 3️⃣: Modify the name of the environmental variable CAMB_NAME on compile_cambq.sh shell script.
[Adapted from Cocoa/installation_scripts/setup_cambq.sh shell script]
#FOLDER="${CAMB_NAME:-"CAMB"}" # Original line - commented
FOLDER="${CAMBQ_NAME:-"CAMB"}"
Step 4️⃣: Add the environmental variables CAMB_URL, CAMB_NAME, and CAMB_GIT_COMMIT to set_installation_options.sh. This is optional if setup_cambq.sh and compile_cambq.sh provide default reasonable values for these variables.
[Adapted from Cocoa/set_installation_options.sh shell script]
export CAMB_URL="https://github.com/cmbant/CAMB"
export CAMB_GIT_COMMIT="45d1c3d27e7480c0f9a82c98522c17ed422dd408"
export CAMB_NAME='CAMB'
# Add and adapt the lines below
export CAMBQ_URL="https://github.com/CAMBQ"
export CAMBQ_GIT_COMMIT="XXX"
export CAMBQ_NAME='CAMBQ'
Step 5️⃣: Add setup_cambq.sh to the list of files run by setup_cocoa.sh as shown below.
[Adapted from Cocoa/setup_cocoa.sh shell script]
declare -a TSCRIPTS=("setup_core_packages.sh"
(...)
"setup_velocileptors.sh"
"setup_cambq.sh)
Step 6️⃣: Add compile_cambq.sh to the list of files run by compile_cocoa.sh as shown below.
[Adapted from Cocoa/compile_cocoa.sh shell script]
declare -a TSCRIPTS=("compile_camb.sh"
(...)
"compile_velocileptors.sh"
"compile_cambq.sh")
Step 7️⃣: Add the following line to the script Cocoa/installation_scripts/flags_impl_unset_keys.sh so these new environmental variables don't pollute the shell session
[Adapted from Cocoa/installation_scripts/flags_impl_unset_keys.sh shell script]
#add the line below
unset -v CAMBQ_URL CAMBQ_GIT_COMMIT CAMBQ_NAME
Adding additional patches to the default CAMB/CLASS is pretty straightforward. Here, we assume the users want to add a patch to modify CAMB (the modified class case is similar).
Step 1️⃣: Copy and save the new patch files to cocoa_installation_libraries/camb_changes.
Step 2️⃣: Modify the setup_cambq.sh shell script as shown below
[Adapted from Cocoa/installation_scripts/setup_camb.sh shell script]
# Patch CAMB to be compatible w/ COCOA environment --------------------------
(...)
# T = TMP
declare -a TFOLDER=("camb/"
"fortran/"
"forutils/"
# Add here the subfolder where the file to be patched is located
) # If nonblank, path must include /
# T = TMP
declare -a TFILE=("_compilers.py"
"Makefile"
"Makefile_compiler"
# Add here the file that needs to be patched
)
#T = TMP, P = PATCH
declare -a TFILEP=("_compilers.patch"
"Makefile.patch"
"Makefile_compiler.patch"
# Add here the file that the patch file
)
To start, we show the current list of CAMB patches below.
cocoa_installation_libraries/camb_changes/camb/_compilers.patch
cocoa_installation_libraries/camb_changes/fortran/Makefile.patch
cocoa_installation_libraries/camb_changes/forutils/Makefile_compiler
Below, we explain what these patches do.
1️⃣ Patch camb/_compilers.patch: This patch modifies the Python functionget_gfortran_version located in the file camb/_compilers.py.
[Adapted from Cocoa/external_modules/code/CAMB/camb/_compilers.py]
def get_gfortran_version(command='gfortran'):
#ver = call_command(command + " -dumpversion") # Original line - commented
# add the line below
ver = call_command("$FORTRAN_COMPILER -dumpversion")
if ver and '.' not in ver:
#ver = call_command(command + " -dumpfullversion") # Original line - commented
# add the line below
ver = call_command("$FORTRAN_COMPILER -dumpfullversion")
return ver
(...)
2️⃣ Patch fortran/Makefile.patch: This patch modifies the file fortran/Makefile.
[Adapted from Cocoa/external_modules/code/CAMB/fortran/Makefile]
#Will detect ifort/gfortran or edit for your compiler # Original line - commented
#ifneq ($(COMPILER),gfortran) # Original line - commented
# ifortErr = $(shell which ifort >/dev/null 2>&1; echo $$?) # Original line - commented
#else # Original line - commented
# ifortErr = 1 # Original line - commented
#endif # Original line - commented
# add the line below
ifortErr = 1
(...)
ifeq "$(ifortErr)" "0"
(...)
else
#gfortErr = $(shell which gfortran >/dev/null; echo $$?) # Original line - commented
# add the line below
gfortErr = 0
ifeq "$(gfortErr)" "0"
#Gfortran compiler (version 6+): # Original line - commented
#compiler_ver = $(shell gfortran -dumpversion 2>&1) # Original line - commented
#COMPILER = gfortran # Original line - commented
#F90C = gfortran # Original line - commented
# add the line below
COMPILER ?= $(FORTRAN_COMPILER)
# add the line below
F90C ?= $(FORTRAN_COMPILER)
(...)
#FFLAGS+=-march=native # Original line - commented
(...)
endif
endif
3️⃣ Patch forutils/Makefile_compiler.patch: This patch modifies the file forutils/Makefile_compiler
[Adapted from Cocoa/external_modules/code/CAMB/forutils/Makefile_compiler]
#ifneq ($(COMPILER),gfortran) # Original line - commented
# ifortErr = $(shell which ifort >/dev/null 2>&1; echo $$?) # Original line - commented
#else # Original line - commented
# ifortErr = 1 # Original line - commented
#endif # Original line - commented
# add the line below
ifortErr = 1
(...)
ifeq "$(ifortErr)" "0"
(...)
else
# major_version = $(shell gfortran -dumpversion 2>&1 | cut -d " " -f 3 | cut -d. -f 1) # Original line - commented
# ifneq ($(shell test $(major_version) -gt 5; echo $$?),0) # Original line - commented
# $(error gfortran version 6.3 or higher (or ifort 14+) is required) # Original line - commented
# endif # Original line - commented
# compiler_ver = $(shell gfortran -dumpversion 2>&1) # Original line - commented
# add the line below
F90C ?= $(FORTRAN_COMPILER)
(...)
endif
To start, we show the current list of CLASS patches below.
cocoa_installation_libraries/class_changes/Makefile.patch
cocoa_installation_libraries/class_changes/python/setup.patch
Below, we explain what these patches do.
1️⃣ Patch Makefile.patch: This patch modifies the file Makefile
[Adapted from Cocoa/external_modules/code/class_public/Makefile]
# your C compiler:
#CC = gcc # Original line - commented
#CC = icc # Original line - commented
#CC = pgcc # Original line - commented
# add the line below
CC ?= $(C_COMPILER)
2️⃣ Patch python/setup.patch: This patch modifies the file python/setup.py
[Adapted from Cocoa/external_modules/code/class_public/python/setup.py]
#GCCPATH_STRING = sbp.Popen( # Original line - commented
# ['gcc -print-libgcc-file-name'], # Original line - commented
# stdout=sbp.PIPE, shell=True).communicate()[0] # Original line - commented
# add the line below
GCCPATH_STRING = sbp.check_output(["$C_COMPILER -print-libgcc-file-name"], shell=True)
(...)
#MVEC_STRING = sbp.Popen( # Original line - commented
# ['gcc', '-lmvec'], # Original line - commented
# stderr=sbp.PIPE).communicate()[1] # Original line - commented
#if b"mvec" not in MVEC_STRING: # Original line - commented
# liblist += ["mvec","m"] # Original line - commented