Hi all,
I need to calculate the virial properties (mass in
particular) of 80,000+ haloes for perhaps up to 25 datasets. Actually,
it's that many haloes at z=0, so fewer for higher z, but you get the
idea. Can you guys suggest the best way to optimize this? My only good
idea is to split up the entries in HopAnalysis.out into multiple files
so each run of HaloProfiler has roughly the same amount of work to do.
Of course, not making projections will speed things up too.
Thanks!
(For those of …
[View More]you getting this message twice, I realized yt-users is the appropriate place for this discussion. Sorry!)
_______________________________________________________
sskory(a)physics.ucsd.edu o__ Stephen Skory
http://physics.ucsd.edu/~sskory/ _.>/ _Graduate Student
________________________________(_)_\(_)_______________
[View Less]
Hi,
I ran into couple of hiccups when using the install script on Ranger,
so I thought I'd share.
The first is that "svn export" doesn't work with the version of
Subversion on Ranger (1.1.4). At least, I'm using it's a version
issue, since the command works on my laptop with version 1.4.6.
Here's the error:
login3$ svn export http://svn.enzotools.org/yt/trunk/doc/
install_script.sh
svn: REPORT request failed on '/yt/!svn/vcc/default'
svn:
Cannot replace a directory from within
I …
[View More]don't think this is very big deal, but it may be worth mentioning
on the Wiki that "wget http://svn.enzotools.org/yt/trunk/doc/
install_script.sh" is a work around. Personally, I find this
preferable, since I really hope I'm not reinstalling so often that I
need to update the script regularly.
The second bump in the road was when it went to build zlib, since
that was the default. I'm not sure that the tried to download the
packages, but the URL http://yt.enzotools.org/dependencies/
zlib-1.2.3.tar.bz2 throws a 404.
Setting YT_DIR=/share/home/00336/rwagner/yt-x86_64/src/yt-trunk-svn/
tar: zlib-1.2.3.tar.bz2: Cannot open: No such file or directory
tar: Error is not recoverable: exiting now
tar: Child returned status 2
tar: Error exit delayed from previous errors
Installing ZLIB
./install_script.sh: line 121: cd: zlib-1.2.3: No such file or directory
Failure. Check /share/home/00336/rwagner/yt-x86_64/yt_install.log.
This was fixed by setting INST_ZLIB=0. Again, not a big deal.
Other than these items, the install went perfectly, and all of the
installed packages seem to be working fine.
--Rick
[View Less]
[install_log trimmed]
So, it seem to me that it is in fact a semi-known issue, where numpy
is using g77 to link and install. Unfortunately, it doesn't seem to
correctly use the "-shared" option. This shows up in the lapack
compilation & linkage step, which is where the install fails.
We can try a couple things here, but unfortunately it might be a
little bit experimental. I will be using the environment variables
you have set in the install_script.sh here for convenience; you'll
need …
[View More]to insert the correct value of DEST_DIR. A lead $ means that
command should be typed in at the prompt.
##
First off, try installing gfortran, if it is not already installed.
$ sudo apt-get install gfortran
Then, if that succeeds:
$ cd $DEST_DIR/src/numpy-1.2.1
$ rm -rf build dist
$ $DEST_DIR/bin/python2.6 setup.py build_ext --fcompiler=gfortran
$ $DEST_DIR/bin/python2.6 setup.py install
If this works, and it might not,
$ touch done
and then re-run the install script. This should pass over most of the
installation and continue on where it left off.
The second option, which I think is less likely to work:
##
$ cd $DEST_DIR/src/numpy-1.2.1/
$ $DEST_DIR/bin/python2.6 setup.py config_fc --f77flags="-shared" built_ext
$ $DEST_DIR/bin/python2.6 setup.py install
and if that works,
$ touch done
and then, again, re-run the install_script.sh.
Let me know how those two options go; hopefully we can figure this
out. If not, I have another idea that I'm a bit reluctant to suggest,
which is to have you "$DEST_DIR/bin/easy_install scons numscons" and
then run "$DEST_DIR/bin/python2.6 setup.py scons install" from the
numpy directory. David Cournapeau has done some amazing work with
scons, and it seems like it will ultimately be the build system for
NumPy (and it's pretty great) but I am hesitant because it requires
two additional dependencies right now.
Let me know how it goes,
-Matt
On Thu, Jan 22, 2009 at 2:33 PM, rsoares <dlleuz(a)xmission.com> wrote:
> Hi Matt,
>
> I have GNU Fortran (GCC) 4.2.4 on Ubuntu and here is the full installation
> log.
> I can use Intel fortran compiler if you think it would help.
>
> Matthew Turk wrote:
>>
>> Hi!
>>
>> Sorry to hear you're having problems, but it's good to hear that
>> you're trying out the newest version, from the trunk. :) I have a
>> suspicion I know what's going on, but it would help out if you could
>> send (even off-list, if you'd rather) the rest of the installation
>> log. What I believe is happening is that the numpy distutils are
>> using the wrong fortran compiler to compile and link the fortran
>> interface libraries. This is a problem I ran into a while back, but
>> my solution was probably not very portable.
>>
>> If we can figure out which fortran compiler you're using, we might be
>> able to make some progress. Are you running on Debian? Can you tell
>> me if you have any of g95, gfortran or g77 installed?
>>
>> Thanks!
>>
>> -Matt
>>
>> On Thu, Jan 22, 2009 at 1:00 PM, rsoares <dlleuz(a)xmission.com> wrote:
>>
[View Less]
> I tried installing yt-1.5 again now that I had python-dev on my system. Got
> the same error.
Oof, I am sorry to hear that. I'll see if I can replicate the problem
on my machine at home, and then get back to you with what I find.
> Please suggest something for my other problem 2.) about not "iyt" in the old
> installation. Here is the successful old-yt install log and the src
> contents that were actually downloaded by the script for that installation.
Okay, iyt is …
[View More]actually a rather simple extension to the functionality
of IPython. (IPython can be "easy_install"'d if you don't have it
already.) It is not necessary, but it does help things out. You can
get the functionality by:
$ ipython -pylab
from yt.mods import *
There are a couple other functions that I've added to iyt, but they
are not terribly useful just yet. Please note that you need
PYTHONPATH set correctly here, or else the "from yt.mods import *"
line won't work for you. I hope this works out -- but if it doesn't,
you can do it all from the regular python interpreter, too, you just
have to plot non-interactively. (I typically do this, myself -- other
people on the list use IPython, but it is not my primary entry point
to yt.) You can plot non-interactively in one window and view the
plots in the other; I've found gqview to be a good application for
this on linux, or even something like firefox!
>
> Meantime I'll see if I can install the whole yt-1.5 by hand.
Good luck, and please let me know if it works for you. It should be
fine if you ahve HDF5, matplotlib, numpy all from the operating
system.
-Matt
[View Less]
Hi,
Two things:
1. I can't get yt-1.5 to finish installing. Hangs with the numpy pkg:
build/temp.linux-i686-2.6/numpy/linalg/lapack_litemodule.o:/ ... more
undefined references to `PyType_IsSubtype\ follow ...
python_xerbla.c:35: undefined reference to `PyErr_SetString' ...
collect2: ld returned 1 exit status
-L/usr/lib/llapack -lblas -lg2c -o
build/lib.linux-i686-2.6/numpy/linalg/lapack_lite.so" failed with exit
status 1
2. The old yt I've been using never did install "iyt" though "…
[View More]yt" has
worked fine.
(it's not in the bin)
I attached a coupled of ref's might be helpful. Thanks for yout time.
Sincerely,
R.Soares
[View Less]
Dear all,
I am currently trying to plot a 2D phase diagram (T vs rho). The plot
is OK, but I have problems with setting the limits of the colorbar
(where CellMassMsun is color-coded). Somehow, they are set
automatically, which is bad, because I need to compare several plots
of different datasets. The set_zlim command does not apparently affect
the plot. I copy here my script, and I hope for some suggestions of
yours.
Thanks in advance,
Luigi
----------
#!/lrz/sys/graphics/yt/…
[View More]1.0/bin/python2.5
# importing modules
from yt.mods import *
import numpy as na
out_dir="/home/hlrb2/h0973/h0973aa/test-runs/test-yt/"
# path for the output of this script
data_dir="/ptmp2/h0973/h0973aa/lss-sgs/64cubed/sgs0/files/outdir/"
# path for ENZO data
#xmin=3e-33
#xmax=3e-26
ymin=5e1
ymax=3e8
zmin=1e4
zmax=1e14
##############################################################################
times = [] # in code units
red = []
# the main cycle over the outputs (if more than one)
pf = lagos.EnzoStaticOutput(data_dir+"RedshiftOutput0014")
red = pf["CosmologyCurrentRedshift"]
print " \n "
print "Analyzing data:"
print "Redshift= "+str(red)
print " \n "
pc = raven.PlotCollection(pf, center=[0.5,0.5,0.5])
pc.set_zlim(zmin,zmax)
pc.add_phase_sphere(1.0,"1", ["Density", "Temperature", "CellMassMsun"],
weight=None, x_bins=128,y_bins=128,#x_bounds=[xmin,xmax],
y_bounds=[ymin,ymax],lazy_reader=True)
#pc.set_zlim(zmin, zmax)
pc.save("l64-sgs0",override=True)
---------------
---------------------------------------------------------------
Luigi Iapichino
Zentrum fuer Astronomie der Universitaet Heidelberg
Institut fuer Theoretische Astrophysik
Albert-Ueberle-Str. 2, D-69120 Heidelberg, Germany
Tel: +49 6221 548983, Fax: +49 6221 544221
e-mail: luigi(a)ita.uni-heidelberg.de
URL: http://www.ita.uni-heidelberg.de/~luigi/
[View Less]