On 11/04/2017 03:41 AM, Ian Hinder wrote:
On 3 Nov 2017, at 19:28, Steven R. Brandt <[email protected]
<mailto:[email protected]>> wrote:
The attached file is the html rendering of a Jupyter notebook version
of Cactus tutorials advocated by Ian and Roland. It is my proposal to
use this going forward.
To run this tutorial, you can either go to the NDS machine (which I
propose should be the default tutorial machine from now on):
https://www.einsteintoolkit.nationaldataservice.org/#/
Alternatively, you may run it in docker.
docker run --name myjupyter -d -p 8888:8888 ndslabs/jupyter-et
If you don't like Jupyter, you can open a console on the NDS machine,
or you can get a command line interface by doing this
docker run -it ndslabs/jupyter-et bash
Which is a machine that already has the requisite cactus packages
installed. You can then use the attached html to enter instructions
one by one.
Please send comments, flames, etc. Thanks.
Hi Steve,
Very nice!
One comment:
- Users probably would like, for their operating system, a single
command that they can copy and paste into their terminal to install
the required packages, rather than going through each of the 23
packages one by one. Also, the table format, while quite attractive,
won't scale to adding columns for more operating systems, such as Mac OS.
I have such a command (see attached). It doesn't yet support Mac (since
I don't use Mac). See attached. It needs some commenting, etc.
Cactus builds without needing to build any external packages on all the
OS's listed (except jpeg on opensuse). Verified by Docker.
As for the scaling of the table, I think all that really needs to be
added is Mac, and we should be able to fit one more column.
One question:
- Is this tutorial in a repository somewhere?
https://github.com/nds-org/jupyter-et
--
Ian Hinder
http://members.aei.mpg.de/ianhin
import os
import re
import sys
def get_pkg_cmd():
for p in os.environ["PATH"].split(os.pathsep):
for cmd in ["apt-get","dnf","yum","zypper"]:
f = p+os.sep+cmd
if os.path.exists(f):
return cmd
pkg_cmd = get_pkg_cmd()
if pkg_cmd == None:
raise Exception("Could not idenfity operating system")
debk = {
"gfortran":"gfortran",
"gcc":"gcc",
"g++":"g++",
"papi":"libpapi-dev",
"gsl":"libgsl-dev",
"lapack":"liblapack-dev",
"hdf5":"libhdf5-dev",
"mpi":[
["libopenmpi-dev","libhdf5-openmpi-dev"],
["libmpich-dev","libhdf5-mpich-dev"],
["libmpich2-dev","libhdf5-mpich2-dev"]],
"pkg-config":"pkg-config",
"subversion":"subversion",
"git":"git",
"python":"python",
"patch":"patch",
"make":"make",
"numa":"numactl",
"hwloc":"libhwloc-dev",
"ssl":"libssl-dev",
"fftw":"libfftw3-dev",
"curl":"curl",
"which":None,
"xargs":None,
"jpeg":"libjpeg-turbo?-dev",
"libtool":None
}
redk = {
"gfortran":"gcc-gfortran",
"gcc":"gcc",
"g++":"gcc-c++",
"papi":"papi-devel",
"gsl":"gsl-devel",
"lapack":"lapack-devel",
"hdf5":"hdf5-devel",
"mpi":[
["openmpi-devel","hdf5-openmpi-devel"],
["mpich-devel","hdf5-mpich-devel"],
["mpich2-devel","hdf5-mpich2-devel"]],
"pkg-config":"pkgconfig",
"subversion":"subversion",
"git":"git",
"python":"python",
"patch":"patch",
"make":"make",
"numa":"numactl-devel",
"hwloc":"hwloc-devel",
"ssl":"openssl-devel",
"fftw":"fftw-devel",
"curl":"curl",
"which":"which", # Used by simfactory
"xargs":"findutils",
"jpeg":"libjpeg-turbo-devel",
"libtool":"libtool-ltdl-devel" # Needed to link on this platform
}
susek = {
"gfortran":"gcc-fortran",
"gcc":"gcc",
"g++":"gcc-c++",
"papi":"papi-devel",
"gsl":"gsl-devel",
"lapack":"lapack-devel",
"hdf5":"hdf5-devel",
"mpi":[
"openmpi-devel",
"mpich-devel",
"mpich2-devel"],
"subversion":"subversion",
"pkg-config":"pkg-config",
"git":"git",
"python":"python",
"patch":"patch",
"make":"make",
"numa":"libnuma-devel",
"hwloc":"hwloc-devel",
"ssl":"libopenssl-devel",
"fftw":"libfftw3-3",
"curl":"curl",
"which":"which",
"xargs":None,
"jpeg":None,
"libtool":None
}
# Check that both tables have the same keys
def check(h1,h2):
for k in h1:
assert k in h2, k
for k in h2:
assert k in h1, k
check(debk,redk)
check(redk,susek)
install_cache = {}
def installed1(cmd):
global install_cache
if type(cmd) == list:
install_count = 0
missing = []
for c in cmd:
res = installed1(c);
install_count += res["installed"]
missing += res["missing"]
return {"installed":install_count,"missing":missing}
if pkg_cmd == "apt-get":
if cmd in install_cache:
return install_cache[cmd]
ex = (os.system("dpkg -s "+cmd) == 0)
install_cache[cmd] = ex
if ex:
return {"installed":1,"missing":[]}
if pkg_cmd == "yum" or pkg_cmd == "dnf" or pkg_cmd == "zypper":
if install_cache == {}:
install_cache = {}
for pkg in os.popen("rpm -qa"):
one_pkg = re.sub("-[^-]+-[^-]+$","",pkg)
install_cache[one_pkg]=1
if cmd in install_cache:
return {"installed":1,"missing":[]}
return {"installed":0,"missing":[cmd]}
def installed(cmd):
if type(cmd) == str:
return installed1(cmd)
elif type(cmd) == list:
answer = None
for c in cmd:
res = installed1(c)
nin = len(res["missing"])
ins = res["installed"]
if nin==0:
return res
elif answer == None:
answer = res
elif ins > answer["installed"]:
answer = res
elif ins == answer["installed"] and nin < len(answer["missing"]):
answer = res
return answer
return {"installed":0,"missing":[]}
pkgs = None
if pkg_cmd == "apt-get":
pkgs = debk
elif pkg_cmd == "dnf" or pkg_cmd == "yum":
pkgs = redk
elif pkg_cmd == "zypper":
pkgs = susek
else:
raise Exception("No package manager")
if pkgs == None:
raise Exception("Could not determine what packages to install")
def install():
answer={"installed":0,"missing":[]}
for k in pkgs:
p = pkgs[k]
res = installed(p)
answer["installed"] += res["installed"]
answer["missing"] += res["missing"]
if len(answer["missing"]) == 0:
sys.stdout.write("# All packages are installed\n")
else:
# Special thing for Centos
if os.path.exists("/etc/centos-release"):
epel = installed("epel-release")
if len(epel["missing"]) > 0:
sys.stdout.write(pkg_cmd+" install -y epel-release\n")
fd = open("install-for-cactus.sh","w")
fd.write(pkg_cmd)
fd.write(" install -y")
for c in answer["missing"]:
if type(c) == str:
if type(c) == str:
fd.write(' ')
fd.write(c)
elif type(c) == list:
for cc in c:
fd.write(' ')
fd.write(cc)
else:
raise Exception()
fd.write("\n")
fd.close()
sys.stdout.write("Install file 'install-for-cactus.sh' has been written\n")
def gets(c,k):
pre = c+" install -y "
if type(k) == str:
return pre+k
elif type(k) == list:
if type(k[0]) == list:
return " ".join(k[0])
elif type(k[0]) == str:
return pre+k[0]
else:
raise Exception()
elif type(k) == type(None):
return " "
else:
raise Exception(str(type(k)))
if __name__ == "__main__":
if len(sys.argv)>1 and sys.argv[1] == "--table":
fd = open("install-for-cactus.html","w")
fd.write("<table>\n");
fd.write("<tr><th>Package</th><th>Debian/Mint/Ubuntu</th>"+
"<th>fedora</th><th>centos</th><th>opensuse</th></tr>\n")
for k in debk:
fd.write('<tr>')
fd.write("<td>"+k+"</td>")
fd.write("<td>"+gets("apt-get",debk[k])+"</td>")
fd.write("<td>"+gets("dnf",redk[k])+"</td>")
fd.write("<td>"+gets("yum",redk[k])+"</td>")
fd.write("<td>"+gets("zypper",susek[k])+"</td>")
fd.write("</tr>\n")
fd.write("</table>\n")
fd.close()
sys.stdout.write("Install file 'install-for-cactus.html' has been written\n")
else:
install()
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