Add preliminary BoxLib based backend. #438

memmett · 2014-07-14T18:06:10Z

This PR adds preliminary support for a state backend based on BoxLib. To use this backend you need to install PyBoxLib:

git clone https://ccse.lbl.gov/pub/Downloads/BoxLib.git
cd BoxLib/Src/Python
python setup.py install --user

Next, create a symlink in clawpack/clawpack to the boxclaw module:

cd clawpack/clawpack
ln -s ../../pyclaw/src/boxclaw boxclaw

Now you should be good to go!

cd clawpack/pyclaw/examples/acoustics_1d_homogeneous
python acoustics_1d.py use_boxlib=True

…om_aux.

Conflicts: examples/acoustics_1d_homogeneous/acoustics_1d.py examples/advection_1d/advection_1d.py

…ied. Fix domain decomposition.

Conflicts: examples/acoustics_1d_homogeneous/acoustics_1d.py examples/acoustics_3d_variable/acoustics_3d_interface.py examples/advection_1d/advection_1d.py examples/advection_2d/advection_2d.py src/pyclaw/solution.py

ahmadia · 2014-07-14T18:16:47Z

The structure of this looks good. I think we will need to set up a corresponding PR in clawpack/clawpack to properly incorporate BoxClaw, and I can also set up a hashdist build to verify this.

I'd also like to see at least one or two regression tests before we merge this. Is there any documentation outside of the examples?

coveralls · 2014-07-14T18:47:37Z

Coverage decreased (-0.03%) when pulling df096d2 on memmett:boxlib into e646b1a on clawpack:master.

memmett · 2014-07-14T19:28:09Z

I will get some regression tests running... do they need to be MPI enabled at this stage?

ahmadia · 2014-07-14T19:31:52Z

No.

On Mon, Jul 14, 2014 at 12:28 PM, Matthew Emmett notifications@github.com
wrote:

I will get some regression tests running... do they need to be MPI enabled
at this stage?

—
Reply to this email directly or view it on GitHub
#438 (comment).

ketch · 2014-07-14T19:33:31Z

src/boxclaw/README

@@ -0,0 +1,17 @@
+


I think if you rename boxclaw/README to boxclaw/README.rst, Github will render it for you.

ketch · 2014-07-14T19:34:17Z

Yeah, serial is fine for now -- it will be great to have this available.

coveralls · 2014-07-14T20:43:05Z

Coverage decreased (-0.04%) when pulling 309fe78 on memmett:boxlib into e646b1a on clawpack:master.

coveralls · 2014-07-14T20:49:53Z

Coverage decreased (-0.04%) when pulling d13de03 on memmett:boxlib into e646b1a on clawpack:master.

…d advection_1d examples.

memmett · 2014-07-14T21:00:30Z

I have added two regression tests. The easiest (fewest lines of code) way to do this was by monkey patching the build_variant_arg_dicts routine in pyclaw.utils. A better long term solution should probably be worked out when BoxClaw becomes a first (second?) class citizen of PyClaw.

coveralls · 2014-07-14T21:26:19Z

Coverage decreased (-0.11%) when pulling 2fbf81e on memmett:boxlib into e646b1a on clawpack:master.

ketch · 2014-07-16T14:23:39Z

There are some hardcode paths that need to be modified in order for BoxLib to compile:

Line 5 of Src/Python/GNUmakefile_CXX.mak should point to the directory from which you cloned BoxLib
You must set MPIHOME to the location of your MPI installation in Tools/F_mk/GMakeMPI.mak b/Tools/F_mk/GMakeMPI.mak

After I did that, I did compile some files, but I got the following error at what I believe is the linking step:

mpif90 -shared -o build/temp.macosx-10.5-x86_64-2.7/_bl1.so o/1d.Darwin.g++.gfortran.MPI.EXE/BoxLib.o o/1d.Darwin.g++.gfortran.MPI.EXE/ParmParse.o o/1d.Darwin.g++.gfortran.MPI.EXE/Utility.o o/1d.Darwin.g++.gfortran.MPI.EXE/UseCount.o o/1d.Darwin.g++.gfortran.MPI.EXE/DistributionMapping.o o/1d.Darwin.g++.gfortran.MPI.EXE/ParallelDescriptor.o o/1d.Darwin.g++.gfortran.MPI.EXE/VisMF.o o/1d.Darwin.g++.gfortran.MPI.EXE/Arena.o o/1d.Darwin.g++.gfortran.MPI.EXE/BArena.o o/1d.Darwin.g++.gfortran.MPI.EXE/CArena.o o/1d.Darwin.g++.gfortran.MPI.EXE/FabConv.o o/1d.Darwin.g++.gfortran.MPI.EXE/FPC.o o/1d.Darwin.g++.gfortran.MPI.EXE/Box.o o/1d.Darwin.g++.gfortran.MPI.EXE/IntVect.o o/1d.Darwin.g++.gfortran.MPI.EXE/IndexType.o o/1d.Darwin.g++.gfortran.MPI.EXE/Orientation.o o/1d.Darwin.g++.gfortran.MPI.EXE/RealBox.o o/1d.Darwin.g++.gfortran.MPI.EXE/BoxList.o o/1d.Darwin.g++.gfortran.MPI.EXE/BoxArray.o o/1d.Darwin.g++.gfortran.MPI.EXE/BoxDomain.o o/1d.Darwin.g++.gfortran.MPI.EXE/FArrayBox.o o/1d.Darwin.g++.gfortran.MPI.EXE/IArrayBox.o o/1d.Darwin.g++.gfortran.MPI.EXE/BaseFab.o o/1d.Darwin.g++.gfortran.MPI.EXE/MultiFab.o o/1d.Darwin.g++.gfortran.MPI.EXE/iMultiFab.o o/1d.Darwin.g++.gfortran.MPI.EXE/FabArray.o o/1d.Darwin.g++.gfortran.MPI.EXE/CoordSys.o o/1d.Darwin.g++.gfortran.MPI.EXE/Geometry.o o/1d.Darwin.g++.gfortran.MPI.EXE/COORDSYS_1D.o o/1d.Darwin.g++.gfortran.MPI.EXE/SPECIALIZE_1D.o o/1d.Darwin.g++.gfortran.MPI.EXE/BLutil_F.o o/1d.Darwin.g++.gfortran.MPI.EXE/BLParmParse_F.o o/1d.Darwin.g++.gfortran.MPI.EXE/BLBoxLib_F.o o/1d.Darwin.g++.gfortran.MPI.EXE/boxlib_wrap_1.o  -lstdc++
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ld: symbol(s) not found for architecture x86_64
collect2: error: ld returned 1 exit status
make[1]: *** [build/temp.macosx-10.5-x86_64-2.7/_bl1.so] Error 1
make: *** [all] Error 2
********************************************************************************
error: can't copy 'build/temp.macosx-10.5-x86_64-2.7/_bl1.so': doesn't exist or not a regular file

memmett · 2014-07-16T17:29:50Z

Oops, didn't notice that hardcoded path -- I will make it relative. Unfortunately I don't have access to an OSX machine, so wasn't able to test the build step on a Mac. Looking at the comments in GMakeMPI.mak, it looks like you need to set your MPIHOME environment variable before building. Finally, are you using GNU compilers? It looks as though the -shared flag isn't doing what I'd expect it to do...

ketch · 2014-07-17T00:31:02Z

Yes, I'm using GNU compilers.

ketch · 2014-08-13T21:52:25Z

Src/Python - [master●] » export MPICH_CXX=/usr/local/bin/g++-4.8
Src/Python - [master●] » mpic++ --version
g++-4.8 (Homebrew gcc 4.8.3_1) 4.8.3
Copyright (C) 2013 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

ketch · 2014-08-13T21:54:28Z

and here's a bit of the error message I currently get:

make -f GNUmakefile_CXX.mak DIM=1 OUT=build/temp.macosx-10.5-x86_64-2.7
Compiling FArrayBox.cpp ...
mpic++ -Wno-deprecated -ftemplate-depth-64 -g -O3  -DMPICH_IGNORE_CXX_SEEK -fPIC -D__USE_XOPEN2K8 -DNDEBUG -DBL_USE_MPI -DMPICH_SKIP_MPICXX -DBL_GCC_VERSION='4.2.1' -DBL_GCC_MAJOR_VERSION=4 -DBL_GCC_MINOR_VERSION=2 -DBL_SPACEDIM=1 -DBL_FORT_USE_UNDERSCORE -DBL_Darwin  -I/usr/local/bin/include -I/usr/local/bin/include -I. -Isrc -I/Users/ketch/BoxLib/Src/C_BaseLib -I/Users/ketch/anaconda/include/python2.7 -I/Users/ketch/anaconda/lib/python2.7/site-packages/numpy/core/include -c  /Users/ketch/BoxLib/Src/C_BaseLib/FArrayBox.cpp -o o/1d.Darwin.g++-4.8.gfortran.MPI.EXE/FArrayBox.o
/Users/ketch/BoxLib/Src/C_BaseLib/FArrayBox.cpp: In member function 'bool FArrayBox::contains_nan() const':
/Users/ketch/BoxLib/Src/C_BaseLib/FArrayBox.cpp:171:24: error: 'isnan' was not declared in this scope
         if (isnan(*dp++))

memmett · 2014-08-13T22:35:11Z

I just pushed a change to pull in isinf and isnan from std if you are using Darwin. Can you pull and subsequently

rm -rf build d f o
export MPICH_CXX=/usr/local/bin/g++-4.8
python setup.py build

ketch · 2014-08-14T00:09:15Z

Hooray! I have a BoxLib installation now.

I followed the other instructions (by the way, there is an extra "../" in your softlink). I tried to run the acoustics example, but I get

python(20582) malloc: *** error for object 0x7fff7645f570: pointer being freed was not allocated

I have verified that this happens somewhere in the call

logger.info("max_sizes: " + str(max_sizes))

in boxlib/geometry.py. It also happens if I go into the debugger there and just ask for str(max_sizes).

ketch · 2014-08-14T00:10:37Z

I tried disabling that logger message but I still get a malloc error somewhere shortly after.

memmett · 2014-08-14T03:20:16Z

Progress! I will try the acoustics example again (been a while) and see if I can recreate your malloc error.

memmett · 2014-08-14T19:40:42Z

I am unable to recreate any memory issues on my machines. I have requested a repurposed Mac from LBL, so should have access to an OSX box soon. I will ask for 10.8.5 and see if it is available. Let me know if there are any other things about your environment that I should be aware of. Will keep you posted.

ketch · 2014-08-14T19:54:50Z

Okay, there probably are other things, but I'm not aware of them ;-)

This macbook is a little messed up; somehow I uninstalled the App Store and
can't get it back, so it's impossible to update the OS.

Anyway, I can try with a couple of other machines when I get back to KAUST
in a few days.

On Thu, Aug 14, 2014 at 8:40 PM, Matthew Emmett notifications@github.com
wrote:

I am unable to recreate any memory issues on my machines. I have requested
a repurposed Mac from LBL, so should have access to an OSX box soon. I will
ask for 10.8.5 and see if it is available. Let me know if there are any
other things about your environment that I should be aware of. Will keep
you posted.

—
Reply to this email directly or view it on GitHub
#438 (comment).

ketch · 2014-08-26T13:12:50Z

Working on a different machine now, I did

cd ~/Research/Software
git clone https://ccse.lbl.gov/pub/Downloads/BoxLib.git
cd BoxLib/Src/Python
export MPIHOME=/usr/local/opt/mpich2
python setup.py install --user

and got the same error @mandli gets (recursive template depth).

memmett · 2014-09-11T03:04:28Z

Just an update, the lab IT dept finally got around to providing me with a re-purposed OSX machine with 10.8.5 on it. Hope to get things running soon... will keep you posted.

memmett · 2014-09-15T18:06:09Z

@ketch @mandli After some tweaks to BoxLib makefiles, I can now install PyBoxLib on OSX 10.8.5 using:

gcc 4.9 (homebrew) + anaconda
gcc 4.9 (homebrew) + mpich2 + default system python (2.7.5)
clang (system default) + mpich2 + gfortran (homebrew) + system python

I have tried to minimize the number of environment variables that the user has to set when running "python setup.py build" for PyBoxLib.

Futher notes are here: https://gist.github.com/memmett/d00df480fb9034f0a2d2

I hope this works on your machines!

mandli · 2014-09-16T21:30:43Z

I will try this out, I am surprised that nothing specific needed to be done to get clang to work though. Maybe this is an ABI issue?

memmett · 2014-09-16T22:06:38Z

To be clear, I had to tweak the make files to get clang to compile BoxLib. Once this was fixed everything else went smoothly.

ketch · 2014-10-12T12:03:17Z

I tried it again, and have now completely messed up the compilers on my system (I'm getting ld: library not found for -lgfortran)...I believe this is due to my ignorance and nothing related to BoxLib.

ahmadia · 2014-10-12T15:09:50Z

On Sun, Oct 12, 2014 at 8:03 AM, David Ketcheson notifications@github.com
wrote:

m getting ld: library not found for -lgfortran

The gfortran compilers on OS X can be a bit tricky. Feel free to ping me
by email if you need some help sorting them out.

…-merge Conflicts: examples/acoustics_1d_homogeneous/acoustics_1d.py examples/acoustics_1d_homogeneous/test_acoustics.py examples/advection_1d/test_advection.py

coveralls · 2014-11-10T06:25:25Z

Coverage decreased (-0.07%) when pulling 414250e on memmett:boxlib into 9426db9 on clawpack:master.

ketch · 2014-11-10T15:51:23Z

@memmett Did you say that there is a hashdist or conda install for this now?

ketch · 2014-11-13T07:24:14Z

I have successfully run this now, using hashdist. Here is what I believe I had to do:

git clone https://github.com/hashdist/hashdist
export PATH=${PWD}/hashdist/bin:${PATH}
hit build -v https://gist.githubusercontent.com/ahmadia/fd665650c484266dc9c2/raw/e47717d525b44a59a8424835d4f1eda0ba407287/clawpack.Darwin.yaml

Then I edited the yaml file, commenting out the clawpack part. Next I did

hit develop clawpack.Darwin.yaml
export PATH=~/clawpack.Darwin/bin:${PATH}
easy_install pip
hash -r

Then I went to my clawpack directory and did

pip install -e .
cd pyclaw/examples/advection_1d/
python advection_1d.py use_boxclaw=1

coveralls · 2014-11-17T21:04:22Z

Coverage decreased (-0.0%) when pulling 085c8dd on memmett:boxlib into 9426db9 on clawpack:master.

coveralls · 2014-11-24T22:07:48Z

Coverage decreased (-0.07%) when pulling a45d61a on memmett:boxlib into 9195d83 on clawpack:master.

memmett · 2015-01-28T22:28:42Z

Just pushed some fixes to BoxLib. Now I can get this running by doing:

wget https://gist.githubusercontent.com/memmett/84d42ce52af31ac75008/raw/ecd814c39599448240e9112e6cf32a19156f3144/clawpack-boxlib-dev.yaml
hit build clawpack-boxlib-dev.yaml
export PATH=$PWD/clawpack-boxlib-dev/bin:$PATH

Then, cd into my clawpack directory and:

pip install -e .
cd pyclaw/examples/advection_1d/
python advection_1d.py use_boxlib=1

You may need to tweak the HashDist profile that I created above to suite your machine. I'd like to rearrange the mapping between the PyClaw AMR (grid, patch etc) constructs and the BoxLib constructs, but figure we should get this merged first.

ketch · 2015-03-08T13:47:09Z

I tried the latest installation instructions and got this (after updating my installation of hashdist to 0.3):

~ » hit build clawpack-boxlib-dev.yaml
[blas] Building blas/orqin7luuh5d, follow log with:
[blas]   tail -f /Users/ketch/.hashdist/tmp/blas-orqin7luuh5d/build.log
Downloading http://releases.nixos.org/patchelf/patchelf-0.8/patchelf-0.8.tar.bz2...
Downloading 'http://releases.nixos.org/patchelf/patchelf-0.8/patchelf-0.8.tar.bz2'
[=========================] 100.0% (0.1MB of 0.1MB) 0.010MB/s ETA 0s
[patchelf] Building patchelf/k3rloj265ogt, follow log with:
[patchelf]   tail -f /Users/ketch/.hashdist/tmp/patchelf-k3rloj265ogt/build.log
[bzip2] Building bzip2/yhn7t7sdxdfd, follow log with:
[bzip2]   tail -f /Users/ketch/.hashdist/tmp/bzip2-yhn7t7sdxdfd/build.log
[bzip2 ERROR] Command '[u'/bin/bash', '_hashdist/build.sh']' returned non-zero exit status 2
[bzip2 ERROR] command failed (code=2); raising

ahmadia · 2015-03-08T15:18:55Z

@ketch - are you on OS X? You'll want to change the line where it says debian to osx. Sorry that there isn't a better way to do this right now, but all profiles are hard-coded to a specific operating system.

ketch · 2015-03-11T05:20:19Z

@ahmadia Thanks. I should have been suspicious of that line. After setting it to osx, I got a lot further. But eventually I get the same linking errors about Undefined symbols for architecture x86_64: that I got back on July 16, 2014 (see above).

ahmadia · 2015-03-11T05:32:00Z

Okay, that error is likely due to you being unable to link against Python libraries. I think @memmett may have had to hardcode library link flags in to do the right thing.

HashDist automatically creates a build log for you when a build fails, and this usually can provide enough hints to figure out how to fix things. Can you paste the failed build log somewhere like gist.github.com?

ahmadia · 2015-03-11T05:35:10Z

FWIW, I think https://gist.github.com/memmett/d00df480fb9034f0a2d2#file-boxclaw-osx-txt-L68 was the link problem he may have been referring to. Even posting the complete error message helps.

Matthew Emmett added 14 commits April 15, 2014 14:05

Add BoxClaw.

769464b

BoxClaw: Fix rollaxis for multi-dimensions, tidy and add get_auxbc_fr…

b2de466

…om_aux.

BoxClaw: Add 'multifab' write routine.

91217e6

BoxClaw: Add 'use_boxlib' arguments.

d2aa5ad

Merge branch 'master' of github.com:clawpack/pyclaw into boxlib-merge

f5cd753

Conflicts: examples/acoustics_1d_homogeneous/acoustics_1d.py examples/advection_1d/advection_1d.py

Check for 'multifab' in format_list in Solution.write.

2348d04

Add 'use_boxlib' to acoustics_3d example.

aa7aaf6

BoxClaw: Fix lower/upper bounds of patches.

31699ae

BoxClaw: Add logging to geometry module. Don't let patches be deepcop…

37a7d59

…ied. Fix domain decomposition.

BoxClaw: Fix Header in boxclaw.io.write so that VisIt works.

d558d19

BoxClaw: Add README and tidy up a bit.

da0687c

BoxClaw: Tidy (remove commented block).

d64ec40

BoxClaw: Fix domain decomposition logic in 1D.

aa50fcd

Merge branch 'upstream' into boxlib-merge2

df096d2

Conflicts: examples/acoustics_1d_homogeneous/acoustics_1d.py examples/acoustics_3d_variable/acoustics_3d_interface.py examples/advection_1d/advection_1d.py examples/advection_2d/advection_2d.py src/pyclaw/solution.py

ketch reviewed Jul 14, 2014
View reviewed changes

src/boxclaw/README

@@ -0,0 +1,17 @@

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ketch Jul 14, 2014

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I think if you rename boxclaw/README to boxclaw/README.rst, Github will render it for you.

Matthew Emmett added 2 commits July 14, 2014 13:13

boxlib: Revert whitespace changes and rename README to README.rst.

309fe78

boxlib: Revert whitespace changes in solution.py.

d13de03

boxlib: Add BoxClaw regressions tests for acoustics_1d_homogeneous an…

2fbf81e

…d advection_1d examples.

Merge branch 'master' of git://github.com/clawpack/pyclaw into boxlib…

414250e

…-merge Conflicts: examples/acoustics_1d_homogeneous/acoustics_1d.py examples/acoustics_1d_homogeneous/test_acoustics.py examples/advection_1d/test_advection.py

BoxClaw: Finish move to Fortran based BoxLib.

a45d61a

memmett force-pushed the boxlib branch from 085c8dd to a45d61a Compare November 24, 2014 21:38

mandli mentioned this pull request May 3, 2015

Release candidate 5.3.0 alpha clawpack/clawpack#63

Closed

Add preliminary BoxLib based backend. #438

Are you sure you want to change the base?

Add preliminary BoxLib based backend. #438

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