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ucvm_setup.py
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ucvm_setup.py
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#!/usr/bin/env python
#
# This is the install script for the UCVM software framework.
# This work in conjuction with scripts in the largefiles directory. The largefile scripts will download and distribute
# the required large files before this ucvm_setup script is run.
#
#
import os
import sys
import getopt
from subprocess import call, Popen, PIPE
import json
import platform
import socket
import shlex
# Variables
# Set the version number for the installation script.
VERSION = "22.7.0"
# User defined variables.
all_flag = False
dynamic_flag = True
restart_flag = False
use_iobuf = False
## control adding of explicit dynamic linker flag
user_dynamic_flag = False
## track how many requeted models needs gfortran
needs_gfortran = 1
skip_ask_path = False
# Should we abort after testing system conditions?
error_out = False
modelsToInstall = []
librariesToInstall = []
modelPaths = {}
unsupported_features = []
shell_script = ""
# Print usage.
def usage():
print("Automatically sets up UCVMC and alerts the user to potential complications.\n")
print("\t-s --static Use static linking.")
print("\t-d --dynamic Use dynamic linking.")
print("\t-a --all Use all available models.")
print("\t-r --restart This is a restart of ucvm_setup.py call.")
print("\t-p --path use supplied installation path.")
print("\t-h --help usage.\n")
print("UCVMC %s\n" % VERSION)
# Stands for "error gracefully". Prints out a message for the error and asks to contact [email protected].
def eG(err, step):
print("\nERROR:")
print("An error occurred while trying to setup UCVM. Specifically, the error was:\n")
print(str(err))
print("\nAt step: %s\n" % step)
print("Please contact [email protected] for assistance setting up UCVM. In your message,")
print("please let us know the operating system on which you are running and some")
print("specifications about your computer.\n")
exit(1)
# Find out if we have certain executables installed.
def which(file):
for path in os.environ["PATH"].split(":"):
if os.path.exists(path + "/" + file):
return path + "/" + file
return None
# Records the command to the global shell script variable.
def callAndRecord(command, nocall = False):
global shell_script
print(' ==> command used.. '+'_'.join(command))
if nocall == False:
retVal = call(command)
if not retVal == 0:
eG("Error executing command.", command)
shell_script += command[0]
for cmd in command[1:]:
shell_script += " \"" + cmd + "\""
shell_script += "\n"
# Prints a pretty text version of a tuple list.
def printPretty(list):
buffer = ""
# Make a nice comma list.
for i in range(0, len(list)):
buffer += list[i]
if i < len(list) - 2:
buffer += ", "
elif i == len(list) - 2 and len(list) != 2:
buffer += ", and "
elif i == len(list) - 2:
buffer += " and "
print(buffer)
# create matching install directory from the build directory
# base on configure's prefix
def createInstallTargetPath( targetpath ):
print('ADDING '+targetpath)
if not os.path.exists(targetpath):
call(["mkdir", "-p", targetpath])
# Install with the configure, make, make install paradigm.
#
# This makes three assumptions
# (1) All required tar files are in the current_working_directory/work directory, and are gzipped
# (2) All installs of type "model" go to ucvmpath/model
# (3) All installs of type "library" go to ucvmpath/lib
#
def installConfigMakeInstall(tarname, ucvmpath, type, config_data):
global needs_gfortran
print("\nInstalling " + type + " " + tarname)
pathname = "lib"
if type == "model":
pathname = "model"
workpath = "./work/" + pathname
strip_level = "2"
if config_data["Path"] == "fftw" or \
config_data["Path"] == "proj-5" or \
config_data["Path"] == "euclid3" or \
config_data["Path"] == "netcdf" or \
config_data["Path"] == "hdf5" or \
config_data["Path"] == "curl":
strip_level = "1"
## skip the models that already exists and go to the ones that did not get processed yet
## still needs to track needs_gfortran
if "Requirements" in config_data:
requirements_array= config_data["Requirements"]
if "gfortran" in requirements_array:
needs_gfortran += 1
if(restart_flag) :
test_path= workpath + "/" + config_data["Path"];
if os.path.exists(test_path):
print("\nSkip building " + config_data["Path"]);
return
#
# We need to un-tar the file.
# The strip level determines how much of the path found in the tar file are removed.
# strip=1 will remove the proj-5.0.0/configure and output only configure.in
# This enables us to untar into drictories with static names like proj-5
#
print("Decompressing " + type)
callAndRecord(["mkdir", "-p", workpath + "/" + config_data["Path"]])
callAndRecord(["tar", "zxvf", workpath + "/" + tarname, "-C", workpath + "/" + config_data["Path"], \
"--strip", strip_level])
savedPath = os.getcwd()
os.chdir(workpath + "/" + config_data["Path"])
callAndRecord(["cd", workpath + "/" + config_data["Path"]], True)
#
# proj-5 library is an exception. It does not require use of aclocal, only ./configure
#
if not config_data["Path"] == "proj-5":
print("\nRunning aclocal")
aclocal_array = ["aclocal"]
if os.path.exists("./m4"):
aclocal_array += ["-I", "m4"]
callAndRecord(aclocal_array)
print("\nRunning automake")
callAndRecord(["automake", "--add-missing", "--force-missing"])
print("\nRunning autoconf")
callAndRecord(["autoconf"])
print("\nRunning ./configure")
configure_array = ["./configure", "--prefix=" + ucvmpath + "/" + pathname + "/" + config_data["Path"]]
createInstallTargetPath( ucvmpath + "/" + pathname + "/" + config_data["Path"])
if "Libraries" in config_data:
needs_array = config_data["Libraries"]
if "euclid3" in needs_array:
configure_array.append("--with-etree-lib-path=" + ucvmpath + "/lib/euclid3/lib")
configure_array.append("--with-etree-include-path=" + ucvmpath + "/lib/euclid3/include")
if "proj-5" in needs_array:
configure_array.append("--with-proj4-lib-path=" + ucvmpath + "/lib/proj-5/lib")
configure_array.append("--with-proj4-include-path=" + ucvmpath + "/lib/proj-5/include")
if config_data["Path"] == "cencal":
configure_array.append("LDFLAGS=-L" + ucvmpath + "/lib/euclid3/lib -L" + ucvmpath + "/lib/proj-5/lib")
configure_array.append("CPPFLAGS=-I" + ucvmpath + "/lib/euclid3/include -I" + ucvmpath + "/lib/proj-5/include")
elif config_data["Path"] == "netcdf":
configure_array.append("LDFLAGS=-L" + ucvmpath + "/lib/hdf5/lib")
configure_array.append("CPPFLAGS=-I" + ucvmpath + "/lib/hdf5/include")
if "CompileFlags" in config_data:
configure_array += config_data["CompileFlags"].split(" ")
callAndRecord(configure_array)
print("\nRunning make clean")
callAndRecord(["make", "clean"])
print("\nRunning make")
if config_data["Path"] == "cencal":
os.chdir("./libsrc")
callAndRecord(["make"])
else:
callAndRecord(["make"])
print("\nInstalling...")
callAndRecord(["make", "install"])
if config_data["Path"] == "cencal":
os.chdir("../")
callAndRecord(["mkdir", "-p", ucvmpath + "/model/" + config_data["Path"] + "/model"])
callAndRecord(["mv", "./model/USGSBayAreaVM-08.3.0.etree", ucvmpath + "/model/" + config_data["Path"] + "/model/"])
callAndRecord(["mv", "./model/USGSBayAreaVMExt-08.3.0.etree", ucvmpath + "/model/" + config_data["Path"] + "/model/"])
config_data["Install"]="true"
os.chdir(savedPath)
callAndRecord(["cd", savedPath], True)
## create the ucvm_env.sh that is approriate to go into /etc/profile.d/
##
def _add2LIBRARYPATH_bash(modelsToInstall, librariesToInstall) :
str="add2LD_LIBRARY_PATH ${UCVM_INSTALL_PATH}/lib/euclid3/lib\n"
str=str+"add2DYLD_LIBRARY_PATH ${UCVM_INSTALL_PATH}/lib/euclid3/lib\n"
str=str+"add2LD_LIBRARY_PATH ${UCVM_INSTALL_PATH}/lib/proj-5/lib\n"
str=str+"add2DYLD_LIBRARY_PATH ${UCVM_INSTALL_PATH}/lib/proj-5/lib\n"
if "CS173" in modelsToInstall:
str=str+"add2LD_LIBRARY_PATH ${UCVM_INSTALL_PATH}/model/cs173/lib\n"
str=str+"add2DYLD_LIBRARY_PATH ${UCVM_INSTALL_PATH}/model/cs173/lib\n"
if "CS173H" in modelsToInstall:
str=str+"add2LD_LIBRARY_PATH ${UCVM_INSTALL_PATH}/model/cs173h/lib\n"
str=str+"add2DYLD_LIBRARY_PATH ${UCVM_INSTALL_PATH}/model/cs173hlib\n"
if "CVM-H" in modelsToInstall:
str=str+"add2LD_LIBRARY_PATH ${UCVM_INSTALL_PATH}/model/cvmh/lib\n"
str=str+"add2DYLD_LIBRARY_PATH ${UCVM_INSTALL_PATH}/model/cvmh/lib\n"
if "CVMHLABN" in modelsToInstall:
str=str+"add2LD_LIBRARY_PATH ${UCVM_INSTALL_PATH}/model/cvmhlabn/lib\n"
str=str+"add2DYLD_LIBRARY_PATH ${UCVM_INSTALL_PATH}/model/cvmhlabn/lib\n"
if "CVMHSGBN" in modelsToInstall:
str=str+"add2LD_LIBRARY_PATH ${UCVM_INSTALL_PATH}/model/cvmhsgbn/lib\n"
str=str+"add2DYLD_LIBRARY_PATH ${UCVM_INSTALL_PATH}/model/cvmhsgbn/lib\n"
if "CVMHVBN" in modelsToInstall:
str=str+"add2LD_LIBRARY_PATH ${UCVM_INSTALL_PATH}/model/cvmhvbn/lib\n"
str=str+"add2DYLD_LIBRARY_PATH ${UCVM_INSTALL_PATH}/model/cvmhvbn/lib\n"
if "CVMHSMBN" in modelsToInstall:
str=str+"add2LD_LIBRARY_PATH ${UCVM_INSTALL_PATH}/model/cvmhsmbn/lib\n"
str=str+"add2DYLD_LIBRARY_PATH ${UCVM_INSTALL_PATH}/model/cvmhsmbn/lib\n"
if "CVMHSBCBN" in modelsToInstall:
str=str+"add2LD_LIBRARY_PATH ${UCVM_INSTALL_PATH}/model/cvmhsbcbn/lib\n"
str=str+"add2DYLD_LIBRARY_PATH ${UCVM_INSTALL_PATH}/model/cvmhsbcbn/lib\n"
if "CVMHSBBN" in modelsToInstall:
str=str+"add2LD_LIBRARY_PATH ${UCVM_INSTALL_PATH}/model/cvmhsbbn/lib\n"
str=str+"add2DYLD_LIBRARY_PATH ${UCVM_INSTALL_PATH}/model/cvmhsbbn/lib\n"
if "CVMHSTBN" in modelsToInstall:
str=str+"add2LD_LIBRARY_PATH ${UCVM_INSTALL_PATH}/model/cvmhstbn/lib\n"
str=str+"add2DYLD_LIBRARY_PATH ${UCVM_INSTALL_PATH}/model/cvmhstbn/lib\n"
if "CVMHRBN" in modelsToInstall:
str=str+"add2LD_LIBRARY_PATH ${UCVM_INSTALL_PATH}/model/cvmhrbn/lib\n"
str=str+"add2DYLD_LIBRARY_PATH ${UCVM_INSTALL_PATH}/model/cvmhrbn/lib\n"
if "CVMHIBBN" in modelsToInstall:
str=str+"add2LD_LIBRARY_PATH ${UCVM_INSTALL_PATH}/model/cvmhibbn/lib\n"
str=str+"add2DYLD_LIBRARY_PATH ${UCVM_INSTALL_PATH}/model/cvmhibbn/lib\n"
if "CVM-S4" in modelsToInstall:
str=str+"add2LD_LIBRARY_PATH ${UCVM_INSTALL_PATH}/model/cvms/lib\n"
str=str+"add2DYLD_LIBRARY_PATH ${UCVM_INSTALL_PATH}/model/cvms/lib\n"
if "WFCVM" in modelsToInstall:
str=str+"add2LD_LIBRARY_PATH ${UCVM_INSTALL_PATH}/model/wfcvm/lib\n"
str=str+"add2DYLD_LIBRARY_PATH ${UCVM_INSTALL_PATH}/model/wfcvm/lib\n"
if "IMPERIAL" in modelsToInstall:
str=str+"add2LD_LIBRARY_PATH ${UCVM_INSTALL_PATH}/model/ivlsu/lib\n"
str=str+"add2DYLD_LIBRARY_PATH ${UCVM_INSTALL_PATH}/model/ivlsu/lib\n"
if "COACHELLA" in modelsToInstall:
str=str+"add2LD_LIBRARY_PATH ${UCVM_INSTALL_PATH}/model/cvlsu/lib\n"
str=str+"add2DYLD_LIBRARY_PATH ${UCVM_INSTALL_PATH}/model/cvlsu/lib\n"
if "ALBACORE" in modelsToInstall:
str=str+"add2LD_LIBRARY_PATH ${UCVM_INSTALL_PATH}/model/albacore/lib\n"
str=str+"add2DYLD_LIBRARY_PATH ${UCVM_INSTALL_PATH}/model/albacore/lib\n"
if "CVM-S4.26" in modelsToInstall:
str=str+"add2LD_LIBRARY_PATH ${UCVM_INSTALL_PATH}/model/cvms5/lib\n"
str=str+"add2DYLD_LIBRARY_PATH ${UCVM_INSTALL_PATH}/model/cvms5/lib\n"
if "CVM-S4.26.M01" in modelsToInstall:
str=str+"add2LD_LIBRARY_PATH ${UCVM_INSTALL_PATH}/model/cvmsi/lib\n"
str=str+"add2DYLD_LIBRARY_PATH ${UCVM_INSTALL_PATH}/model/cvmsi/lib\n"
if "CenCalVM" in modelsToInstall:
str=str+"add2LD_LIBRARY_PATH ${UCVM_INSTALL_PATH}/model/cencal/lib\n"
str=str+"add2DYLD_LIBRARY_PATH ${UCVM_INSTALL_PATH}/model/cencal/lib\n"
if "CCA" in modelsToInstall:
str=str+"add2LD_LIBRARY_PATH ${UCVM_INSTALL_PATH}/model/cca/lib\n"
str=str+"add2DYLD_LIBRARY_PATH ${UCVM_INSTALL_PATH}/model/cca/lib\n"
if "NetCDF" in librariesToInstall:
str=str+"add2LD_LIBRARY_PATH ${UCVM_INSTALL_PATH}/lib/netcdf/lib\n"
str=str+"add2DYLD_LIBRARY_PATH ${UCVM_INSTALL_PATH}/lib/netcdf/lib\n"
str=str+"add2LD_LIBRARY_PATH ${UCVM_INSTALL_PATH}/lib/hdf5/lib\n"
str=str+"add2DYLD_LIBRARY_PATH ${UCVM_INSTALL_PATH}/lib/hdf5/lib\n"
return str
def _add2path_bash(master):
str = "function add2"+master+"() {\n"
str = str +" if [ \"$"+master+"\" ] ; then\n"
str = str +" if ! echo \"$"+master+"\" | grep -Eq \"(^|:)$1($|:)\" ; then\n"
str = str +" if [ \"$2\" = \"after\" ] ; then\n"
str = str +" export "+master+"=\"$"+master+":$1\"\n"
str = str +" else\n"
str = str +" export "+master+"=\"$1:$"+master+"\"\n"
str = str +" fi\n"
str = str +" fi\n"
str = str +" else\n"
str = str +" export "+master+"=\"$1\"\n"
str = str +" fi\n"
str = str +"}\n"
return str
def makeBashScript(ucvmsrc, ucvmpath, modelsToInstall, librariesToInstall) :
str=""
fp=open("conf/ucvm_env.sh","w")
fp.write("## \n")
fp.write("## models: [")
for x in modelsToInstall:
fp.write(" ")
fp.write(x)
fp.write(" ]")
fp.write("\n")
fp.write("## libraries: [")
for x in librariesToInstall:
fp.write(" ")
fp.write(x)
fp.write(" ]")
fp.write("\n")
fp.write("## \n")
fp.write("\n")
str="export UCVM_SRC_PATH=" +ucvmsrc
fp.write(str)
fp.write("\n")
str="export UCVM_INSTALL_PATH="+ucvmpath.rstrip("/")
fp.write(str)
fp.write("\n")
fp.write("\n")
pstr=_add2path_bash("PATH")
fp.write(pstr)
fp.write("\n")
pstr=_add2path_bash("LD_LIBRARY_PATH")
fp.write(pstr)
fp.write("\n")
pstr=_add2path_bash("DYLD_LIBRARY_PATH")
fp.write(pstr)
fp.write("\n")
pstr=_add2path_bash("PYTHONPATH")
fp.write(pstr)
fp.write("\n")
ldpstr=_add2LIBRARYPATH_bash(modelsToInstall, librariesToInstall)
fp.write(ldpstr)
## add to PYTHONPATH
pstr="add2PYTHONPATH ${UCVM_INSTALL_PATH}/utilities/pycvm"
fp.write(pstr)
fp.write("\n")
## add to PATH
pstr="add2PATH ${UCVM_INSTALL_PATH}/bin"
fp.write(pstr)
fp.write("\n")
pstr="add2PATH ${UCVM_INSTALL_PATH}/utilities"
fp.write(pstr)
fp.write("\n")
fp.close();
## create the ucvm_env.py that is python script can be import to make sure
## LD_LIBRARY_PATH and DYLD_LIBRARY_PATH is setup up
##
def _add2LIBRARYPATH_python(modelsToInstall, librariesToInstall) :
str=" add2LD_LIBRARY_PATH(UCVM_INSTALL_PATH +\"/lib/euclid3/lib\")\n"
str=str+" add2DYLD_LIBRARY_PATH(UCVM_INSTALL_PATH + \"/lib/euclid3/lib\")\n"
str=str+" add2LD_LIBRARY_PATH(UCVM_INSTALL_PATH + \"lib/proj-5/lib\")\n"
str=str+" add2DYLD_LIBRARY_PATH(UCVM_INSTALL_PATH + \"lib/proj-5/lib\")\n"
if "CS173" in modelsToInstall:
str=str+" add2LD_LIBRARY_PATH(UCVM_INSTALL_PATH + \"model/cs173/lib\")\n"
str=str+" add2DYLD_LIBRARY_PATH(UCVM_INSTALL_PATH + \"model/cs173/lib\")\n"
if "CS173H" in modelsToInstall:
str=str+" add2LD_LIBRARY_PATH(UCVM_INSTALL_PATH + \"model/cs173h/lib\")\n"
str=str+" add2DYLD_LIBRARY_PATH(UCVM_INSTALL_PATH + \"model/cs173hlib\")\n"
if "CVM-H" in modelsToInstall:
str=str+" add2LD_LIBRARY_PATH(UCVM_INSTALL_PATH + \"model/cvmh/lib\")\n"
str=str+" add2DYLD_LIBRARY_PATH(UCVM_INSTALL_PATH + \"model/cvmh/lib\")\n"
if "CVMHLABN" in modelsToInstall:
str=str+" add2LD_LIBRARY_PATH(UCVM_INSTALL_PATH + \"model/cvmhlabn/lib\")\n"
str=str+" add2DYLD_LIBRARY_PATH(UCVM_INSTALL_PATH + \"model/cvmhlabn/lib\")\n"
if "CVMHSGBN" in modelsToInstall:
str=str+" add2LD_LIBRARY_PATH(UCVM_INSTALL_PATH + \"model/cvmhsgbn/lib\")\n"
str=str+" add2DYLD_LIBRARY_PATH(UCVM_INSTALL_PATH + \"model/cvmhsgbn/lib\")\n"
if "CVMHVBN" in modelsToInstall:
str=str+" add2LD_LIBRARY_PATH(UCVM_INSTALL_PATH + \"model/cvmhvbn/lib\")\n"
str=str+" add2DYLD_LIBRARY_PATH(UCVM_INSTALL_PATH + \"model/cvmhvbn/lib\")\n"
if "CVMHSMBN" in modelsToInstall:
str=str+" add2LD_LIBRARY_PATH(UCVM_INSTALL_PATH + \"model/cvmhsmbn/lib\")\n"
str=str+" add2DYLD_LIBRARY_PATH(UCVM_INSTALL_PATH + \"model/cvmhsmbn/lib\")\n"
if "CVMHSBCBN" in modelsToInstall:
str=str+" add2LD_LIBRARY_PATH(UCVM_INSTALL_PATH + \"model/cvmhsbcbn/lib\")\n"
str=str+" add2DYLD_LIBRARY_PATH(UCVM_INSTALL_PATH + \"model/cvmhsbcbn/lib\")\n"
if "CVMHSBBN" in modelsToInstall:
str=str+" add2LD_LIBRARY_PATH(UCVM_INSTALL_PATH + \"model/cvmhsbbn/lib\")\n"
str=str+" add2DYLD_LIBRARY_PATH(UCVM_INSTALL_PATH + \"model/cvmhsbbn/lib\")\n"
if "CVMHSTBN" in modelsToInstall:
str=str+" add2LD_LIBRARY_PATH(UCVM_INSTALL_PATH + \"model/cvmhstbn/lib\")\n"
str=str+" add2DYLD_LIBRARY_PATH(UCVM_INSTALL_PATH + \"model/cvmhstbn/lib\")\n"
if "CVMHRBN" in modelsToInstall:
str=str+" add2LD_LIBRARY_PATH(UCVM_INSTALL_PATH + \"model/cvmhrbn/lib\")\n"
str=str+" add2DYLD_LIBRARY_PATH(UCVM_INSTALL_PATH + \"model/cvmhrbn/lib\")\n"
if "CVMHIBBN" in modelsToInstall:
str=str+" add2LD_LIBRARY_PATH(UCVM_INSTALL_PATH + \"model/cvmhibbn/lib\")\n"
str=str+" add2DYLD_LIBRARY_PATH(UCVM_INSTALL_PATH + \"model/cvmhibbn/lib\")\n"
if "CVM-S4" in modelsToInstall:
str=str+" add2LD_LIBRARY_PATH(UCVM_INSTALL_PATH + \"model/cvms/lib\")\n"
str=str+" add2DYLD_LIBRARY_PATH(UCVM_INSTALL_PATH + \"model/cvms/lib\")\n"
if "WFCVM" in modelsToInstall:
str=str+" add2LD_LIBRARY_PATH(UCVM_INSTALL_PATH + \"model/wfcvm/lib\")\n"
str=str+" add2DYLD_LIBRARY_PATH(UCVM_INSTALL_PATH + \"model/wfcvm/lib\")\n"
if "IMPERIAL" in modelsToInstall:
str=str+" add2LD_LIBRARY_PATH(UCVM_INSTALL_PATH + \"model/ivlsu/lib\")\n"
str=str+" add2DYLD_LIBRARY_PATH(UCVM_INSTALL_PATH + \"model/ivlsu/lib\")\n"
if "COACHELLA" in modelsToInstall:
str=str+" add2LD_LIBRARY_PATH(UCVM_INSTALL_PATH + \"model/cvlsu/lib\")\n"
str=str+" add2DYLD_LIBRARY_PATH(UCVM_INSTALL_PATH + \"model/cvlsu/lib\")\n"
if "ALBACORE" in modelsToInstall:
str=str+" add2LD_LIBRARY_PATH(UCVM_INSTALL_PATH + \"model/albacore/lib\")\n"
str=str+" add2DYLD_LIBRARY_PATH(UCVM_INSTALL_PATH + \"model/albacore/lib\")\n"
if "CVM-S4.26" in modelsToInstall:
str=str+" add2LD_LIBRARY_PATH(UCVM_INSTALL_PATH + \"model/cvms5/lib\")\n"
str=str+" add2DYLD_LIBRARY_PATH(UCVM_INSTALL_PATH + \"model/cvms5/lib\")\n"
if "CVM-S4.26.M01" in modelsToInstall:
str=str+" add2LD_LIBRARY_PATH(UCVM_INSTALL_PATH + \"model/cvmsi/lib\")\n"
str=str+" add2DYLD_LIBRARY_PATH(UCVM_INSTALL_PATH + \"model/cvmsi/lib\")\n"
if "CenCalVM" in modelsToInstall:
str=str+" add2LD_LIBRARY_PATH(UCVM_INSTALL_PATH + \"model/cencal/lib\")\n"
str=str+" add2DYLD_LIBRARY_PATH(UCVM_INSTALL_PATH + \"model/cencal/lib\")\n"
if "CCA" in modelsToInstall:
str=str+" add2LD_LIBRARY_PATH(UCVM_INSTALL_PATH + \"model/cca/lib\")\n"
str=str+" add2DYLD_LIBRARY_PATH(UCVM_INSTALL_PATH + \"model/cca/lib\")\n"
if "NetCDF" in librariesToInstall:
str=str+" add2LD_LIBRARY_PATH(UCVM_INSTALL_PATH + \"lib/netcdf/lib\")\n"
str=str+" add2DYLD_LIBRARY_PATH(UCVM_INSTALL_PATH + \"lib/netcdf/lib\")\n"
str=str+" add2LD_LIBRARY_PATH(UCVM_INSTALL_PATH + \"lib/hdf5/lib\")\n"
str=str+" add2DYLD_LIBRARY_PATH(UCVM_INSTALL_PATH + \"lib/hdf5/lib\")\n"
return str
def _add2path_python():
str = "def _add2env(PNAME, path) :\n"
str = str +" my_path=my_env.get(PNAME,False)\n"
str = str +" if my_path != False :\n"
str = str +" if my_path.find(path) != -1 :\n"
str = str +" my_path = my_path + \":\" + path\n"
str = str +" else :\n"
str = str +" my_path = path\n"
str = str +" my_env[PNAME] = my_path\n\n"
str = str +"def add2PATH(path) :\n"
str = str +" _add2env(\"PATH\",path)\n\n"
str = str +"def add2LD_LIBRARY_PATH(path) :\n"
str = str +" _add2env(\"LD_LIBRARY_PATH\",path)\n\n"
str = str +"def add2DYLD_LIBRARY_PATH(path) :\n"
str = str +" _add2env(\"DYLD_LIBRARY_PATH\",path)\n\n"
return str
def makePythonScript(ucvmsrc, ucvmpath, modelsToInstall, librariesToInstall) :
str=""
fp=open("conf/ucvm_env.py","w")
fp.write("## \n")
fp.write("## models: [")
for x in modelsToInstall:
fp.write(" ")
fp.write(x)
fp.write(" ]")
fp.write("\n")
fp.write("## libraries: [")
for x in librariesToInstall:
fp.write(" ")
fp.write(x)
fp.write(" ]\n")
fp.write("## \n\n")
str="import os\n"
fp.write(str)
str="UCVM_SRC_PATH=\"" + ucvmsrc + "\"\n"
fp.write(str)
str="UCVM_INSTALL_PATH=\""+ucvmpath.rstrip("/")+"\"\n"
fp.write(str)
str="my_env=os.environ\n\n"
fp.write(str)
pstr=_add2path_python()
fp.write(pstr)
str="def setup_ucvm_env():\n"
fp.write(str)
ldpstr=_add2LIBRARYPATH_python(modelsToInstall, librariesToInstall)
fp.write(ldpstr)
## add to PATH
pstr=" add2PATH(UCVM_INSTALL_PATH + \"bin\")\n"
fp.write(pstr)
pstr=" add2PATH(UCVM_INSTALL_PATH + \"utilities\")\n"
fp.write(pstr)
fp.close();
def _addInstallNameTool_bash(modelsToInstall, librariesToInstall):
str=""
if "Euclid3" in librariesToInstall:
str=str+"install_name_tool -change libetree.so ${MY_UCVM_INSTALL_PATH}/lib/euclid3/lib/libetree.so $1\n"
if "CS173" in modelsToInstall:
str=str+"install_name_tool -change libcs173.so ${MY_UCVM_INSTALL_PATH}/model/cs173/lib/libcs173.so $1\n"
if "CS173H" in modelsToInstall:
str=str+"install_name_tool -change libcs173h.so ${MY_UCVM_INSTALL_PATH}/model/cs173h/lib/libcs173h.so $1\n"
if "CVM-H" in modelsToInstall:
str=str+"install_name_tool -change libcvmh.so ${MY_UCVM_INSTALL_PATH}/model/cvmh/lib/libcvmh.so $1\n"
if "CVMHLABN" in modelsToInstall:
str=str+"install_name_tool -change libcvmhlabn.so ${MY_UCVM_INSTALL_PATH}/model/cvmhlabn/lib/libcvmhlabn.so $1\n"
if "CVMHSGBN" in modelsToInstall:
str=str+"install_name_tool -change libcvmhsgbn.so ${MY_UCVM_INSTALL_PATH}/model/cvmhsgbn/lib/libcvmhsgbn.so $1\n"
if "CVMHVBN" in modelsToInstall:
str=str+"install_name_tool -change libcvmhvbn.so ${MY_UCVM_INSTALL_PATH}/model/cvmhvbn/lib/libcvmhvbn.so $1\n"
if "CVMHSMBN" in modelsToInstall:
str=str+"install_name_tool -change libcvmhsmbn.so ${MY_UCVM_INSTALL_PATH}/model/cvmhsmbn/lib/libcvmhsmbn.so $1\n"
if "CVMHSBCBN" in modelsToInstall:
str=str+"install_name_tool -change libcvmhsbcbn.so ${MY_UCVM_INSTALL_PATH}/model/cvmhsbcbn/lib/libcvmhsbcbn.so $1\n"
if "CVMHSBBN" in modelsToInstall:
str=str+"install_name_tool -change libcvmhsbbn.so ${MY_UCVM_INSTALL_PATH}/model/cvmhsbbn/lib/libcvmhsbbn.so $1\n"
if "CVMHSTBN" in modelsToInstall:
str=str+"install_name_tool -change libcvmhstbn.so ${MY_UCVM_INSTALL_PATH}/model/cvmhstbn/lib/libcvmhstbn.so $1\n"
if "CVMHRBN" in modelsToInstall:
str=str+"install_name_tool -change libcvmhrbn.so ${MY_UCVM_INSTALL_PATH}/model/cvmhrbn/lib/libcvmhrbn.so $1\n"
if "CVMHIBBN" in modelsToInstall:
str=str+"install_name_tool -change libcvmhibbn.so ${MY_UCVM_INSTALL_PATH}/model/cvmhibbn/lib/libcvmhibbn.so $1\n"
if "CVM-S4" in modelsToInstall:
str=str+"install_name_tool -change libcvms.so ${MY_UCVM_INSTALL_PATH}/model/cvms/lib/libcvms.so $1\n"
if "WFCVM" in modelsToInstall:
str=str+"install_name_tool -change libwfcvm.so ${MY_UCVM_INSTALL_PATH}/model/wfcvm/lib/libwfcvm.so $1\n"
if "IMPERIAL" in modelsToInstall:
str=str+"install_name_tool -change libivlsu.so ${MY_UCVM_INSTALL_PATH}/model/ivlsu/lib/libivlsu.so $1\n"
if "COACHELLA" in modelsToInstall:
str=str+"install_name_tool -change libcvlsu.so ${MY_UCVM_INSTALL_PATH}/model/cvlsu/lib/libcvlsu.so $1\n"
if "ALBACORE" in modelsToInstall:
str=str+"install_name_tool -change libalbacore.so ${MY_UCVM_INSTALL_PATH}/model/albacore/lib/libalbacore.so $1\n"
if "CVM-S4.26" in modelsToInstall:
str=str+"install_name_tool -change libcvms5.so ${MY_UCVM_INSTALL_PATH}/model/cvms5/lib/libcvms5.so $1\n"
if "CVM-S4.26.M01" in modelsToInstall:
str=str+"install_name_tool -change libcvmsi.so ${MY_UCVM_INSTALL_PATH}/model/cvmsi/lib/libcvmsi.so $1\n"
if "CenCalVM" in modelsToInstall:
str=str+"install_name_tool -change libcencal.so ${MY_UCVM_INSTALL_PATH}/model/cencal/lib/libcencal.so $1\n"
if "CCA" in modelsToInstall:
str=str+"install_name_tool -change libcca.so ${MY_UCVM_INSTALL_PATH}/model/cca/lib/libcca.so $1\n"
return str
def makeDyLibNameChangeScript(ucvmsrc, ucvmpath, modelsToInstall, librariesToInstall) :
str=""
fp=open("conf/call_install_name_tool","w")
fp.write("#!/bin/bash \n")
fp.write("## \n")
fp.write("## models: [")
for x in modelsToInstall:
fp.write(" ")
fp.write(x)
fp.write(" ]")
fp.write("\n")
fp.write("## libraries: [")
for x in librariesToInstall:
fp.write(" ")
fp.write(x)
fp.write(" ]")
fp.write("\n")
fp.write("## \n")
fp.write("## workaround for macOS's system-integrity-protection's handling\n")
fp.write("## of DYLD/LD_LIBRARY_PATH\n")
fp.write("## \n")
fp.write("\n")
str="export MY_UCVM_SRC_PATH=" +ucvmsrc
fp.write(str)
fp.write("\n")
str="export MY_UCVM_INSTALL_PATH="+ucvmpath.rstrip("/")
fp.write(str)
fp.write("\n")
ldpstr=_addInstallNameTool_bash(modelsToInstall, librariesToInstall)
fp.write(ldpstr)
fp.close()
def process_user_path(p):
global ucvmpath
ucvmpath = p
## link proj-5's library to PROJ_LIB location if PROJ_LIB is defined
def linkPROJ_5(ucvmpath) :
try :
proj_lib = os.environ['PROJ_LIB']
except:
return
call(["ln", "-p", ucvmpath+"/lib/proj-5/lib/*", proj_lib])
#
# Start of main method.
# Read in the possible arguments
#
try:
opts, args = getopt.getopt(sys.argv[1:], "asdhrp:", ["all", "static", "dynamic", "help", "restart","path"])
except getopt.GetoptError as err:
print(str(err))
usage()
exit(1)
for o, a in opts:
if o in ('-r', '--restart'):
restart_flag = True
print("Restart Flag: True")
elif o in ('-a', '--all'):
all_flag = True
print("All Flag: True")
elif o in ('-s', '--static'):
dynamic_flag = False
print("static Flag: True")
elif o in ('-d', '--dynamic'):
user_dynamic_flag = True
print("dynamic Flag: True")
elif o in ('-p', '--path'):
process_user_path(a)
skip_ask_path = True
elif o in ('-h', '--help'):
usage()
exit(0)
else:
if o[0:6].lower() == "--with-":
unsupported_features.append(o[7:].lower())
else:
print("Invalid option %s" % (o))
exit(1)
print("")
print("UCVM %s Installation" % VERSION)
print("Copyright (C) 20%s University of Southern California. All rights reserved." % (VERSION.split(".")[0]))
print("Using local setup.list and system.list ....")
try:
f = open("./setup/system.list", "r")
json_string = f.read()
f.close()
system_data = json.loads(json_string)
except OSError as e:
eG(e, "Parsing list of supported systems.")
try:
# Check the all-applicable conditions first.
for k, v in system_data["all"].items():
if eval(k):
print("\n" + v["message"])
exec(v["code"])
print("Now check system specific conditions.")
for k in system_data:
print("System_data - k: ", k)
if k != "all" and k in socket.gethostname():
for k2 in sorted(system_data[k].iterkeys()):
var_array = system_data[k][k2]
if k2 != "vars":
the_command = Popen([item.replace("\x00", "") for item in shlex.split(var_array["command"])], \
stdout = PIPE, stderr = PIPE)
if var_array["listenOn"] == "stderr":
com_results = the_command.communicate()[1]
else:
com_results = the_command.communicate()[0]
if eval("not " + var_array["condition"] + " com_results"):
print("\n" + var_array["not"])
exit()
else:
for k3, v3 in var_array.items():
if type(v3) is dict:
if not eval(k3) == v3["value"]:
print("\n" + v3["not"])
exec(k3 + " = " + v3["value"])
else:
exec(k3 + " = " + v3)
except Exception as e:
eG(e, "Checking system conditions.")
if error_out == True:
print("\nError(s) encountered. Please resolve the above errors and re-run this script.")
exit(1)
print("Using local setup.list file")
try:
# We now have our list. Parse it.
f = open("./setup/setup.list", "r")
json_string = f.read()
f.close()
config_data = json.loads(json_string)
except OSError as e:
eG(e, "Parsing available model list.")
print("\nPlease answer the following questions to install UCVM.\n")
print("Note that this install and build process may take up to an hour depending on your")
print("computer speed.")
if skip_ask_path == False :
print("Where would you like UCVM to be installed?")
try:
if ucvmpath[0] == "$":
# We want to expand that.
ucvmpath = os.environ(ucvmpath[1:])
except Exception:
# Use default path.
ucvmpath = os.path.expanduser("~")
# Append the version info to the path.
ucvmpath = ucvmpath.rstrip("/") + "/ucvm-" + VERSION
print("(Default: " + ucvmpath + ")")
if sys.version_info.major >= (3) :
enteredpath = input("Enter path or blank to use the default path: ")
else:
enteredpath = raw_input("Enter path or blank to use the default path: ")
if enteredpath.strip() == "":
enteredpath = ucvmpath
while enteredpath != "":
# Check to see that that path exists and is writable.
if not os.access(os.path.dirname(enteredpath.rstrip("/")), os.W_OK | os.X_OK):
print("\n" + enteredpath + " does not exist or is not writable.")
if sys.version_info.major >= (3) :
enteredpath = input("Exiting:Please enter a different path or blank to use the default path: ")
else:
enteredpath = raw_input("Exiting:Please enter a different path or blank to use the default path: ")
sys.exit(0)
else:
break
# Copy final selected path back to the UCVM path variable.
# remove trailing '/' just in case
ucvmpath = enteredpath.rstrip("/")
# Create necessary directories
if not os.path.exists(ucvmpath):
call(["mkdir", "-p", ucvmpath])
call(["mkdir", "-p", ucvmpath+'/work'])
call(["mkdir", "-p", ucvmpath+'/lib'])
## print(config_data["models"].keys())
for model in sorted(iter(config_data["models"].keys()), key=lambda k: config_data["models"][k]["Order"]):
the_model = config_data["models"][model]
tarname = the_model["URL"].split("/")[-1]
ltarname = "./work/model/" + tarname
## continue only if the model is in work_model_dir
if not os.path.isfile(ltarname):
continue
if all_flag == True:
modelsToInstall.append(model)
continue
if config_data["models"][model]["Ask"] != "no":
print("\nWould you like to install " + model + "?")
if sys.version_info.major >= (3) :
dlinstmodel = input("Enter yes or no: ")
else:
dlinstmodel = raw_input("Enter yes or no: ")
if dlinstmodel != "" and dlinstmodel.lower()[0] == "y":
modelsToInstall.append(model)
print("\nYou have indicated that you would like to install")
printPretty(modelsToInstall)
for library in config_data["libraries"]:
the_library = config_data["libraries"][library]
if the_library["Ask"] == "yes" or library.lower() in unsupported_features:
if the_library["Prerequisites"] != "":
if "Dynamic" in the_library["Prerequisites"] and dynamic_flag == False:
print(library + " requires UCVM to be linked dynamically. If you would like " + library)
print("to be included, please re-run ucvm_setup.py with the '-d' flag.")
if "Static" in the_library["Prerequisites"] and dynamic_flag == True:
print(library + " requires UCVM to be linked statically. If you would like " + library)
print("to be included, please re-run ucvm_setup.py without the '-d' flag.")
if library.lower() in unsupported_features:
print("WARNING: " + library + " is unsupported and we cannot guarantee that UCVM")
print("will install correctly on your system if you install it with this library included.")
print("\nWould you like to install support for " + library + "?")
if sys.version_info.major >= (3) :
dlinstlibrary = input("Enter yes or no: ")
else:
dlinstlibrary = raw_input("Enter yes or no: ")
if dlinstlibrary.strip() != "" and dlinstlibrary.strip().lower()[0] == "y":
librariesToInstall.append(library)
elif the_library["Required"] == "yes":
librariesToInstall.append(library)
print("\nYou have indicated that you would like to install")
printPretty(librariesToInstall)
# Check if we can make the work directory.
try:
if not os.path.exists("./work"):
# call(["rm", "-R", "./work"])
# call(["mkdir", "-p", "./work"])
print("Work directory does not exist. Did you remember to stage sources? Error, exitting...")
sys.exit(1)
if not os.path.exists("./work") or not os.access("./work", os.W_OK | os.X_OK):
print("Could not create ./work directory.")
sys.exit(1)
except OSError as e:
eG(e, "Could not create ./work directory.")
print("\nNow setting up the required UCVM libraries...")
for library in config_data["libraries"]:
the_library = config_data["libraries"][library]
if library in librariesToInstall:
if the_library.get("Needs", "") != "":
try:
#downloadWithProgress(config_data["libraries"][the_library["Needs"]]["URL"], "./work/lib", \
# "Downloading" + the_library["Needs"])
tarname = config_data["libraries"][the_library["Needs"]]["URL"].split("/")[-1]
print("Calling Needs Install with tarname,ucvmpath,library:",tarname,ucvmpath)
installConfigMakeInstall(tarname, ucvmpath, "library", config_data["libraries"][the_library["Needs"]])
except Exception as e:
eG(e, "Error installing library " + the_library["Needs"] + " (needed by " + library + ").")
try:
#downloadWithProgress(the_library["URL"], "./work/lib", "Downloading " + library + "..." )
tarname = the_library["URL"].split("/")[-1]
print("Calling URL Install with tarname,ucvmpath,library:",tarname,ucvmpath)
installConfigMakeInstall(tarname, ucvmpath, "library", the_library)
except Exception as e:
eG(e, "Error installing library " + library + ".")
print("\nNow setting up CVM models...")
for model in config_data["models"]:
print("Install model_name: ", model)
the_model = config_data["models"][model]
if model in modelsToInstall:
try:
#
# Currently, this test for existing tar file will always fail because of the
# recursive directory removal done above
# TODO: Change this to check for largefiles/file and copy over if it has been downloaded already
#
tarname = the_model["URL"].split("/")[-1]
ltarname = "./work/model/" + tarname
print("Preparing to install model with tarname: ",tarname)
if not os.path.isfile(ltarname):
print("Model file not found in work directory:",tarname)
print("Exiting...")
sys.exit(1)
else:
print("Model tar file found in work directory:",ltarname)
installConfigMakeInstall(tarname, ucvmpath, "model", the_model)
except Exception as e:
eG(e, "Error installing model " + model + ".")
# Now that the models are installed, we can finally install UCVM!
print("\nInstalling UCVM software...")
print("\nRunning aclocal")
callAndRecord(["aclocal", "-I", "./m4"])
print("\nRunning automake")
callAndRecord(["automake", "--add-missing", "--force-missing"])
print("\nRunning autoconf")
callAndRecord(["autoconf"])
print("\nRunning ./configure for UCVM")
ucvm_conf_command = ["./configure", "--enable-silent-rules", \
"--with-etree-include-path=" + ucvmpath + "/lib/euclid3/include", \
"--with-etree-lib-path=" + ucvmpath + "/lib/euclid3/lib", \
"--with-proj4-include-path=" + ucvmpath + "/lib/proj-5/include", \
"--with-proj4-lib-path=" + ucvmpath + "/lib/proj-5/lib", \
"--with-fftw-include-path=" + ucvmpath + "/lib/fftw/include", \
"--with-fftw-lib-path=" + ucvmpath + "/lib/fftw/lib"]
for model in modelsToInstall:
the_model = config_data["models"][model]
# We need to append the flags.
flag_array = []
flags = the_model["Flags"].split(" ")
for flag in flags:
flag_split = flag.split("=")
if len(flag_split) == 1:
flag_array.append(str(flag))
else:
pathToUse = ucvmpath + "/model/" + the_model["Path"]
if model in modelPaths:
pathToUse = modelPaths[model]
flag_array.append(str(flag_split[0] + "=" + pathToUse + "/" + flag_split[1]))
ucvm_conf_command += flag_array
ucvm_conf_command.append("--prefix=" + ucvmpath)
if dynamic_flag == False:
ucvm_conf_command.append("--enable-static")
if user_dynamic_flag == True:
ucvm_conf_command.append("--enable-dynamic")
if use_iobuf == True:
ucvm_conf_command.append("--enable-iobuf")
if "NetCDF" in librariesToInstall:
ucvm_conf_command.append("--enable-netcdf")
ucvm_conf_command.append("--with-netcdf-include-path=" + ucvmpath + "/lib/netcdf/include")
ucvm_conf_command.append("--with-netcdf-lib-path=" + ucvmpath + "/lib/netcdf/lib")
ucvm_conf_command.append("LDFLAGS=-L" + ucvmpath + "/lib/hdf5/lib")
callAndRecord(ucvm_conf_command)
print("\nMaking UCVM")
callAndRecord(["make", "clean"])
callAndRecord(["make"])
if platform.system() == "Darwin" or platform.system() == "Linux" or dynamic_flag == True:
makeBashScript(os.getcwd(), ucvmpath ,modelsToInstall, librariesToInstall)
makePythonScript(os.getcwd(), ucvmpath ,modelsToInstall, librariesToInstall)
makeDyLibNameChangeScript(os.getcwd(), ucvmpath, modelsToInstall, librariesToInstall)
linkPROJ_5(ucvmpath)
print("\nInstalling UCVM")
callAndRecord(["make", "install"])
print("\nDone installing UCVM!")
sys.stdout.write("\nThank you for installing UCVM.\n")
sys.stdout.flush()
if platform.system() == "Darwin" or platform.system() == "Linux" or dynamic_flag == True:
print("Now edit your ~/.bashrc file to call "+ ucvmpath.rstrip("/") + "/conf/ucvm_env.sh \n")
print(" source " + ucvmpath.rstrip("/") + "/conf/ucvm_env.sh \n")
print("This will set the required UCVM environment variables.")
print("Then log out, and log in, move to tests directory, and run the tests\n")
print(" $ cd " + ucvmpath.rstrip("/") + "/tests ")
print(" $ ./run-testing \n")
print("This will run the UCVM unit and acceptance tests. If all tests pass, ")
print("UCVM is correctly installed and ready to use on your computer.")
print("To try out ucvm, once the tests pass, run an example query.\n")
print(" $ ucvm_query -f "+ ucvmpath+"/conf/ucvm.conf -m cvms < " + ucvmpath+ "/tests/inputs/test_latlons.txt\n")
print("You will then see the following output:\n\nUsing Geo Depth coordinates as default mode.")
print(" -118.0000 34.0000 0.000 280.896 390.000 cvms 696.491 213.000 1974.976 none 0.000 0.000 0.000 crust 696.491 213.000 1974.976")
print(" -118.0000 34.0000 50.000 280.896 390.000 cvms 1669.540 548.000 2128.620 none 0.000 0.000 0.000 crust 1669.540 548.000 2128.620")
print(" -118.0000 34.0000 100.000 280.896 390.000 cvms 1683.174 603.470 2130.773 none 0.000 0.000 0.000 crust 1683.174 603.470 2130.773")
print("-118.0000 34.0000 500.000 280.896 390.000 cvms 3097.562 1656.495 2354.105 none 0.000 0.000 0.000 crust 3097.562 1656.495 2354.105")
print(" -118.0000 34.0000 1000.000 280.896 390.000 cvms 3660.809 2056.628 2443.042 none 0.000 0.000 0.000 crust 3660.809 2056.628 2443.042")
try:
f = open('./setup_log.sh', 'w')
f.write(shell_script)
f.close()
except OSError as e:
eG(e, "Saving setup_log.sh.")
# Write out a installation json file (expanded from setup.list)
try:
f = open('./setup_install.list', 'w')
f.write(json.dumps(config_data,indent=2,sort_keys=True))
f.close()
except OSError as e:
eG(e, "Saving setup_install.list.")
print("\nInstallation complete. Installation log file saved at ./setup_log.sh\n")