[yt-users] Problem when run yt dev in parallel on Blue Waters

Pengfei Chen madcpf at gmail.com
Sun Aug 21 17:09:14 PDT 2016 

Hi Brian and Nathan,

I am trying to install yt-3 on Blue Waters again, since after updating yt
to the current tip it somehow can't run in parallel. When I came to step 3)
following Brian's instructions, I get the following error message:

~/mpi4py-1.3.1 $python setup.py build --mpi=cray
running build
running build_src
running build_py
creating build
creating build/lib.linux-x86_64-2.7
creating build/lib.linux-x86_64-2.7/mpi4py
copying src/rc.py -> build/lib.linux-x86_64-2.7/mpi4py
copying src/__init__.py -> build/lib.linux-x86_64-2.7/mpi4py
creating build/lib.linux-x86_64-2.7/mpi4py/include
creating build/lib.linux-x86_64-2.7/mpi4py/include/mpi4py
copying src/include/mpi4py/mpi4py.MPI.h ->
build/lib.linux-x86_64-2.7/mpi4py/include/mpi4py
copying src/include/mpi4py/mpi4py.MPI_api.h ->
build/lib.linux-x86_64-2.7/mpi4py/include/mpi4py
copying src/include/mpi4py/mpi4py.h ->
build/lib.linux-x86_64-2.7/mpi4py/include/mpi4py
copying src/include/mpi4py/mpi_c.pxd ->
build/lib.linux-x86_64-2.7/mpi4py/include/mpi4py
copying src/include/mpi4py/MPI.pxd ->
build/lib.linux-x86_64-2.7/mpi4py/include/mpi4py
copying src/include/mpi4py/__init__.pxd ->
build/lib.linux-x86_64-2.7/mpi4py/include/mpi4py
copying src/include/mpi4py/__init__.pyx ->
build/lib.linux-x86_64-2.7/mpi4py/include/mpi4py
copying src/include/mpi4py/mpi.pxi ->
build/lib.linux-x86_64-2.7/mpi4py/include/mpi4py
copying src/include/mpi4py/mpi4py.i ->
build/lib.linux-x86_64-2.7/mpi4py/include/mpi4py
copying src/MPI.pxd -> build/lib.linux-x86_64-2.7/mpi4py
copying src/mpi_c.pxd -> build/lib.linux-x86_64-2.7/mpi4py
running build_clib
MPI configuration: [cray] from 'mpi.cfg'
MPI C compiler:    /opt/cray/craype/2.5.4/bin/cc
MPI C++ compiler:  /opt/cray/craype/2.5.4/bin/CC
Traceback (most recent call last):
  File "setup.py", line 588, in <module>
    main()
  File "setup.py", line 585, in main
    run_setup()
  File "setup.py", line 459, in run_setup
    **metadata)
  File "/mnt/a/u/sciteam/madcpf/mpi4py-1.3.1/conf/mpidistutils.py", line
494, in setup
    return fcn_setup(**attrs)
  File "/u/sciteam/madcpf/anaconda2/lib/python2.7/distutils/core.py", line
151, in setup
    dist.run_commands()
  File "/u/sciteam/madcpf/anaconda2/lib/python2.7/distutils/dist.py", line
953, in run_commands
    self.run_command(cmd)
  File "/u/sciteam/madcpf/anaconda2/lib/python2.7/distutils/dist.py", line
972, in run_command
    cmd_obj.run()
  File
"/u/sciteam/madcpf/anaconda2/lib/python2.7/distutils/command/build.py",
line 127, in run
    self.run_command(cmd_name)
  File "/u/sciteam/madcpf/anaconda2/lib/python2.7/distutils/cmd.py", line
326, in run_command
    self.distribution.run_command(command)
  File "/u/sciteam/madcpf/anaconda2/lib/python2.7/distutils/dist.py", line
972, in run_command
    cmd_obj.run()
  File "/mnt/a/u/sciteam/madcpf/mpi4py-1.3.1/conf/mpidistutils.py", line
894, in run
    configure_compiler(self.compiler, config)
  File "/mnt/a/u/sciteam/madcpf/mpi4py-1.3.1/conf/mpidistutils.py", line
249, in configure_compiler
    compiler.compiler += cc_args
TypeError: coercing to Unicode: need string or buffer, list found

Do you have any idea what happens here?

Thanks a lot!
Pengfei

On Mon, Nov 23, 2015 at 12:13 PM, Pengfei Chen <madcpf at gmail.com> wrote:

> Hi Brian,
>
> It works perfectly! Thank you so much!
> I've saved the instructions for later use.
>
> Thanks,
> Pengfei
>
>
> On Fri, Nov 20, 2015 at 3:34 AM, Brian O'Shea <bwoshea at gmail.com> wrote:
>
>> Hi Pengfei,
>>
>> Sorry for the delay in response.  Here are instructions for getting yt-3
>> to work on Blue Waters using mpi4py.  I believe that Rob Sisneros has
>> gotten yt-3 working as a module; however, it is likely that it will not be
>> updated very frequently, at least compared to the pace of yt development.
>>
>> --Brian
>>
>> -----------------------------------------------------------------------
>>
>> Getting yt-3 to work on Blue Waters:
>>
>> 0) Get the GNU software environment set up:  “module swap PrgEnv-cray
>> PrgEnv-gnu” .  This will be necessary later.
>>
>> 1)  Install the Anaconda python distribution (https://store.continuum.io/
>> cshop/anaconda/) for 64-bit Linux systems.  Refresh your path so the
>> Anaconda python’s in your path.
>>
>> 2)  Download mpi4py from https://bitbucket.org/mpi4py/mpi4py/, or grab
>> it from my home directory on Blue Waters (~bwoshea/mpi4py-1.3.1.tar.gz).
>>
>> 3)  Once you’ve unpacked it in your home directory, edit the file
>> mpi.cfg, which is in the top-level mpi4py directory, and add the following
>> chunk of text at the end of the file:
>>
>> [cray]
>> mpicc = cc
>> mpicxx = CC
>> extra_link_args = -shared
>>
>> then, in the top-level mpi4py directory, type:
>>
>> python setup.py build --mpi=cray
>> python setp.py install
>>
>> At this point, you should have a functional version of mpi4py that uses
>> the cray MPI libraries.
>>
>> 4)  You can then install yt via source in your home directory:
>>
>> hg clone https://bitbucket.org/yt_analysis/yt
>> hg update yt
>> python setup.py develop
>>
>> And it should work, though you’re going to need to modify your
>> LD_LIBRARY_PATH to point to your anaconda /lib directory.  You can verify
>> that yt and mpi4py are playing nicely together by running the scripts
>> hw_MPI.py and yt_parallel_test.py, both of which are sitting in my home
>> directory.  (Note that you can do this via batch script or through the
>> interactive queue, both with aprun - you can’t just do it from the login
>> node.)
>>
>> 5) and, optionally, if you want to install Rockstar using yt from source,
>> you do the following:
>>
>> hg clone http://bitbucket.org/MatthewTurk/rockstar
>> cd rockstar
>> hg pull
>> hg up -C tip
>> make lib
>>
>> and *then* make a file called rockstar.cfg that has a single line of
>> text: the path of the rockstar source code directory.  At that point, you
>> need to run “python setup.py develop” again, and yt will recognize that
>> rockstar has been installed and play nicely with it.  You will likely also
>> have to modify your LD_LIBRARY_PATH to point at your rockstar directory so
>> it can find the rockstar library (librockstar.so).
>>
>>
>>
>> On Fri, Nov 20, 2015 at 3:46 AM, Pengfei Chen <madcpf at gmail.com> wrote:
>>
>>> Hi Brian,
>>>
>>> Thank you very much for your reply! No, I followed the instructions here
>>>  http://yt-project.org/docs/dev/installing.html
>>> <http://yt-project.org/docs/dev/installing.html>. I need the
>>> yt-development, but failed when using All-in-One Installation Script to
>>> install it on BW, so I used miniconda to install. Could you please send me
>>> your installation instructions for yt on BW? I will try it out.
>>>
>>> Thanks,
>>> Pengfei
>>>
>>> On Thu, Nov 19, 2015 at 8:45 AM, Brian O'Shea <bwoshea at gmail.com> wrote:
>>>
>>>> Hi Pengfei,
>>>>
>>>> Did you use my installation instructions for yt on Blue Waters?  If
>>>> not, I can send those along.
>>>>
>>>> B
>>>>
>>>>
>>>> On Thu, Nov 19, 2015 at 10:02 AM, Nathan Goldbaum <
>>>> nathan12343 at gmail.com> wrote:
>>>>
>>>>> So it looks like either mpi4py isn't able to properly link against the
>>>>> MPI installation on Blue waters or properly initialize itself at runtime.
>>>>>
>>>>> In either case, this points to the issue being a problem with mpi4py,
>>>>> not yt.
>>>>>
>>>>> Three things to try:
>>>>>
>>>>> * check which version version of mpi4py you have installed in your
>>>>> yt-2.x environment and install that version in your yt-3.x environment. You
>>>>> may have found a bug in mpi4py 2.0, which made major changes to the mpi4py
>>>>> library.
>>>>>
>>>>> * contact the Blue Waters sysadmins.
>>>>>
>>>>> * contact the mpi4py developers
>>>>>
>>>>> Hope that helps,
>>>>>
>>>>> Nathan
>>>>>
>>>>>
>>>>> On Thursday, November 19, 2015, Pengfei Chen <madcpf at gmail.com> wrote:
>>>>>
>>>>>> Hi Nathan,
>>>>>>
>>>>>> Thank you very much for your reply! When I run that test script in
>>>>>> parallel with 16 cores, I get 16 0s. Any suggestions to fix this?
>>>>>>
>>>>>> Thanks,
>>>>>> Pengfei
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Wed, Nov 18, 2015 at 3:40 PM, Nathan Goldbaum <
>>>>>> nathan12343 at gmail.com> wrote:
>>>>>>
>>>>>>> Hi Pengfei,
>>>>>>>
>>>>>>> Can you try to run the following test script in parallel? This will
>>>>>>> determine if the issue is on the yt side of things or the mpi4py side of
>>>>>>> things:
>>>>>>>
>>>>>>>     from mpi4py import MPI
>>>>>>>
>>>>>>>     print(MPI.COMM_WORLD.rank)
>>>>>>>
>>>>>>> -Nathan
>>>>>>>
>>>>>>> On Wed, Nov 18, 2015 at 5:36 PM, Pengfei Chen <madcpf at gmail.com>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> Hi all,
>>>>>>>>
>>>>>>>> I have trouble running yt in parallel on Blue Waters. I installed
>>>>>>>> yt using miniconda, the version of yt is
>>>>>>>>
>>>>>>>> ~/miniconda/lib $yt version
>>>>>>>> yt module located at:
>>>>>>>>     /u/sciteam/madcpf/miniconda/lib/python2.7/site-packages/
>>>>>>>> yt-3.3.dev0-py2.7-linux-x86_64.egg
>>>>>>>> The current version and changeset for the code is:
>>>>>>>> ---
>>>>>>>> Version = 3.3-dev
>>>>>>>> Changeset = 90f900be7a36+ yt
>>>>>>>>
>>>>>>>> Then with miniconda/bin in PATH I installed mpi4py-2.0.0. But when
>>>>>>>> I tried to make the following simple output in parallel, I get:
>>>>>>>>
>>>>>>>> import yt
>>>>>>>> yt.enable_parallelism()
>>>>>>>> from yt.utilities.parallel_tools.parallel_analysis_interface
>>>>>>>> import\
>>>>>>>>  parallel_objects, communication_system
>>>>>>>>
>>>>>>>> comm = communication_system.communicators[-1]
>>>>>>>> print comm.rank, comm.size
>>>>>>>>
>>>>>>>> 0 1
>>>>>>>> 0 1
>>>>>>>> 0 1
>>>>>>>> 0 1
>>>>>>>> 0 1
>>>>>>>> 0 1
>>>>>>>> 0 1
>>>>>>>> 0 1
>>>>>>>> ...
>>>>>>>>
>>>>>>>> When I run a similar code but with yt-2.x also on Blue Waters, I
>>>>>>>> get what I expect:
>>>>>>>>
>>>>>>>> 7 16
>>>>>>>> 15 16
>>>>>>>> 6 16
>>>>>>>> 9 16
>>>>>>>> 11 16
>>>>>>>> 8 16
>>>>>>>> 0 16
>>>>>>>> 4 16
>>>>>>>> ...
>>>>>>>>
>>>>>>>> I'm confused about it. Could anyone give me some suggestions please?
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>> Pengfei
>>>>>>>>
>>>>>>>> _______________________________________________
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>>>>>>>>
>>>>>>>>
>>>>>>>
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