[firedrake] Firedrake Installation
Lee, Suet
suet.lee11 at imperial.ac.uk
Sun Nov 16 14:35:32 GMT 2014
I tried it again for libmpich-dev but it doesn't seem to be installed either.
mosh at ubuntu:~$ dpkg -s libmpich-dev
dpkg-query: package 'libmpich-dev' is not installed and no information is available
Use dpkg --info (= dpkg-deb --info) to examine archive files,
and dpkg --contents (= dpkg-deb --contents) to list their contents.
64bit doesn't work on my laptop for some reason (it's old) - it makes the graphics go funny and I can't see anything.
Suet
________________________________________
From: Florian Rathgeber <florian.rathgeber at imperial.ac.uk>
Sent: 16 November 2014 14:22
To: Lee, Suet; McRae, Andrew
Cc: firedrake
Subject: Re: Firedrake Installation
[Please keep list in CC]
On 16/11/14 14:12, Lee, Suet wrote:
> Not sure if I'm doing it correctly but I tried this:
>
> mosh at ubuntu:~$ dpkg -s mpich2
> dpkg-query: package 'mpich2' is not installed and no information is
> available
> Use dpkg --info (= dpkg-deb --info) to examine archive files,
> and dpkg --contents (= dpkg-deb --contents) to list their contents.
>
> So the problem isn't down to mpich2?
Sorry, the package you want to look for is libmpich-dev
Is there any reason to use a 32bit system? We explicitly do *not*
support 32bit systems and there isn't really a reason not to use 64bit.
Florian
> Suet
>
>
> ------------------------------------------------------------------------
> *From:* Andrew McRae <a.mcrae12 at imperial.ac.uk>
> *Sent:* 16 November 2014 13:41
> *To:* Lee, Suet
> *Subject:* Re: Firedrake Installation
>
> I have no idea, but I've forwarded your problem to the Firedrake mailing
> list; some people on there know a lot more than me about MPI.
>
> On 16 November 2014 13:28, Lee, Suet <suet.lee11 at imperial.ac.uk
> <mailto:suet.lee11 at imperial.ac.uk>> wrote:
>
> I ran the install mpi4py commange but I have a new error now:
>
>
> mosh at ubuntu:~$ wget -O -
> https://github.com/OP2/PyOP2/raw/master/install.sh | sudo bash
> --2014-11-16 13:20:14--
> https://github.com/OP2/PyOP2/raw/master/install.sh
> Resolving github.com <http://github.com> (github.com
> <http://github.com>)... 192.30.252.131
> Connecting to github.com <http://github.com> (github.com
> <http://github.com>)|192.30.252.131|:443... connected.
> HTTP request sent, awaiting response... 302 Found
> Location:
> https://raw.githubusercontent.com/OP2/PyOP2/master/install.sh
> [following]
> --2014-11-16 13:20:16--
> https://raw.githubusercontent.com/OP2/PyOP2/master/install.sh
> Resolving raw.githubusercontent.com
> <http://raw.githubusercontent.com> (raw.githubusercontent.com
> <http://raw.githubusercontent.com>)... 185.31.18.133
> Connecting to raw.githubusercontent.com
> <http://raw.githubusercontent.com> (raw.githubusercontent.com
> <http://raw.githubusercontent.com>)|185.31.18.133|:443... connected.
> HTTP request sent, awaiting response... 200 OK
> Length: 3667 (3.6K) [text/plain]
> Saving to: ‘STDOUT’
>
> 100%[======================================>] 3,667 --.-K/s
> in 0s
>
> 2014-11-16 13:20:16 (40.6 MB/s) - written to stdout [3667/3667]
>
> PyOP2 installation started at Sun Nov 16 13:20:16 GMT 2014
> on Linux ubuntu 3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10
> 19:08:14 UTC 2014 i686 i686 i686 GNU/Linux
>
> *** Privileged installation ***
> Running unprivileged commands as mosh
>
> *** Preparing system ***
>
> *** Installing dependencies ***
>
> *** Installing PETSc ***
>
> *** Installing PyOP2 ***
>
> [ubuntu:31603] *** Process received signal ***
> [ubuntu:31603] Signal: Floating point exception (8)
> [ubuntu:31603] Signal code: Integer divide-by-zero (1)
> [ubuntu:31603] Failing at address: 0xb74d6da0
> [ubuntu:31603] [ 0] [0xb779a40c]
> [ubuntu:31603] [ 1] /usr/lib/i386-linux-gnu/libhwloc.so.5(+0x2cda0)
> [0xb74d6da0]
> [ubuntu:31603] [ 2] /usr/lib/i386-linux-gnu/libhwloc.so.5(+0x2e71c)
> [0xb74d871c]
> [ubuntu:31603] [ 3] /usr/lib/i386-linux-gnu/libhwloc.so.5(+0x2ea8b)
> [0xb74d8a8b]
> [ubuntu:31603] [ 4] /usr/lib/i386-linux-gnu/libhwloc.so.5(+0x98f6)
> [0xb74b38f6]
> [ubuntu:31603] [ 5]
> /usr/lib/i386-linux-gnu/libhwloc.so.5(hwloc_topology_load+0x1c6)
> [0xb74b48ec]
> [ubuntu:31603] [ 6]
> /usr/lib/libopen-rte.so.4(orte_odls_base_open+0x7b1) [0xb76fa881]
> [ubuntu:31603] [ 7]
> /usr/lib/openmpi/lib/openmpi/mca_ess_hnp.so(+0x2445) [0xb7488445]
> [ubuntu:31603] [ 8] /usr/lib/libopen-rte.so.4(orte_init+0x1cf)
> [0xb76cfb3f]
> [ubuntu:31603] [ 9] /usr/lib/libopen-rte.so.4(orte_daemon+0x256)
> [0xb76ec1c6]
> [ubuntu:31603] [10] orted() [0x80485b3]
> [ubuntu:31603] [11]
> /lib/i386-linux-gnu/libc.so.6(__libc_start_main+0xf3) [0xb7504a83]
> [ubuntu:31603] [12] orted() [0x80485f8]
> [ubuntu:31603] *** End of error message ***
> [ubuntu:31601] [[INVALID],INVALID] ORTE_ERROR_LOG: Unable to start a
> daemon on the local node in file ess_singleton_module.c at line 343
> [ubuntu:31601] [[INVALID],INVALID] ORTE_ERROR_LOG: Unable to start a
> daemon on the local node in file ess_singleton_module.c at line 140
> [ubuntu:31601] [[INVALID],INVALID] ORTE_ERROR_LOG: Unable to start a
> daemon on the local node in file runtime/orte_init.c at line 128
> --------------------------------------------------------------------------
> It looks like orte_init failed for some reason; your parallel process is
> likely to abort. There are many reasons that a parallel process can
> fail during orte_init; some of which are due to configuration or
> environment problems. This failure appears to be an internal failure;
> here's some additional information (which may only be relevant to an
> Open MPI developer):
>
> orte_ess_set_name failed
> --> Returned value Unable to start a daemon on the local node
> (-128) instead of ORTE_SUCCESS
> --------------------------------------------------------------------------
> --------------------------------------------------------------------------
> It looks like MPI_INIT failed for some reason; your parallel process is
> likely to abort. There are many reasons that a parallel process can
> fail during MPI_INIT; some of which are due to configuration or
> environment
> problems. This failure appears to be an internal failure; here's some
> additional information (which may only be relevant to an Open MPI
> developer):
>
> ompi_mpi_init: orte_init failed
> --> Returned "Unable to start a daemon on the local node" (-128)
> instead of "Success" (0)
> --------------------------------------------------------------------------
> [ubuntu:31601] *** An error occurred in MPI_Init_thread
> [ubuntu:31601] *** on a NULL communicator
> [ubuntu:31601] *** Unknown error
> [ubuntu:31601] *** MPI_ERRORS_ARE_FATAL: your MPI job will now abort
> --------------------------------------------------------------------------
> An MPI process is aborting at a time when it cannot guarantee that all
> of its peer processes in the job will be killed properly. You should
> double check that everything has shut down cleanly.
>
> Reason: Before MPI_INIT completed
> Local host: ubuntu
> PID: 31601
> --------------------------------------------------------------------------
> PyOP2 installation failed
> See /home/mosh/PyOP2/pyop2_install.log for details
>
> Any idea what's going on?
>
> Suet
>
>
> ------------------------------------------------------------------------
> *From:* Andrew McRae <a.mcrae12 at imperial.ac.uk
> <mailto:a.mcrae12 at imperial.ac.uk>>
> *Sent:* 15 November 2014 23:13
> *To:* Lee, Suet
> *Subject:* Re: Firedrake Installation
>
> Or, if you want to be a guinea pig, don't run the 'sudo pip install
> mpi4py' command and just run the install script again :)
>
> (I updated
> <https://github.com/OP2/PyOP2/commit/e15b3ee8d72369f10c9a84d944a3ecbf06f7e927>
> the script just now -- thanks for alerting us to that bug)
>
> On 15 November 2014 23:09, Andrew McRae <a.mcrae12 at imperial.ac.uk
> <mailto:a.mcrae12 at imperial.ac.uk>> wrote:
>
> Hi Suet,
>
> Sorry about that. This should fix the mpi4py problem: sudo pip
> install mpi4py
>
> Then try the quick install script again.
>
> Yes, PyOP2, FFC, FIAT and UFL need to be installed before
> firerake. However, installing FFC/FIAT/UFL is easy -- you just
> run the 'sudo pip install \ six \ sympy \ ...' command, as
> described on http://www.firedrakeproject.org/download.html.
>
> Let me know if there's any other problems.
>
> Best,
>
> Andrew
>
>
> On 15 November 2014 23:00, Lee, Suet <suet.lee11 at imperial.ac.uk
> <mailto:suet.lee11 at imperial.ac.uk>> wrote:
>
> Hi Andrew,
>
>
> So I finally got round to the Firedrake installation!
>
>
> I'm trying to install PyOP2. The only problem is that I'm
> running up against the following error:
>
>
> PyOP2 installation started at Sat Nov 15 22:38:45 GMT 2014
> on Linux ubuntu 3.13.0-24-generic #46-Ubuntu SMP Thu Apr
> 10 19:08:14 UTC 2014 i686 i686 i686 GNU/Linux
>
> *** Privileged installation ***
> Running unprivileged commands as mosh
>
> *** Preparing system ***
>
> *** Installing dependencies ***
>
> *** Installing PETSc ***
>
> *** Installing PyOP2 ***
>
> Traceback (most recent call last):
> File "<string>", line 1, in <module>
> File "pyop2/__init__.py", line 9, in <module>
> from op2 import *
> File "pyop2/op2.py", line 38, in <module>
> import backends
> File "pyop2/backends.py", line 41, in <module>
> from logger import warning
> File "pyop2/logger.py", line 38, in <module>
> from mpi import MPI
> File "pyop2/mpi.py", line 37, in <module>
> from mpi4py import MPI as _MPI
> ImportError: No module named mpi4py
> PyOP2 installation failed
> See /home/mosh/pyop2_install.log for details
>
>
> I must be missing the file mpi4py? Do I have to install
>
> PyOP2 <http://op2.github.io/PyOP2>, FFC
> <https://bitbucket.org/mapdes/ffc>, FIAT
> <https://bitbucket.org/mapdes/fiat>, and UFL
> <https://bitbucket.org/mapdes/ufl>, before Firedrake? I
> attempted the quick installation for PyOP2 but do I need to
> install other packages before that?
>
> Best,
>
> Suet
More information about the firedrake
mailing list