On 16 November 2014 14:22, Rathgeber, Florian < florian.rathgeber@imperial.ac.uk> wrote:
[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@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.
Ah, I wasn't aware of this. Context: Suet got the following error when she tried powering up a 64bit VM, a couple of months ago: "This virtual machine is configured for 64-bit guest operating systems. However, 64-bit operation is not possible. This host does not support Intel VT-x. For more detailed information, see http://vmware.com/info?id=152." [The graphics problem was something different] I guessed that pointing her at the 32bit Ubuntu iso would be easier than making BIOS changes (assuming her processor does support VT-x, but that it's disabled in BIOS). Florian: do you think the problem is related to 32bit-ness? If so, Suet can bring her laptop to Huxley or WPL some time this week and we'll go the 64bit route. Andrew Florian
Suet
------------------------------------------------------------------------ *From:* Andrew McRae <a.mcrae12@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@imperial.ac.uk <mailto:suet.lee11@imperial.ac.uk>> wrote:
I ran the install mpi4py commange but I have a new error now:
mosh@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@imperial.ac.uk <mailto:a.mcrae12@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@imperial.ac.uk <mailto:a.mcrae12@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@imperial.ac.uk <mailto:suet.lee11@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
On 16/11/14 14:39, Andrew McRae wrote:
On 16 November 2014 14:22, Rathgeber, Florian <florian.rathgeber@imperial.ac.uk <mailto:florian.rathgeber@imperial.ac.uk>> wrote:
[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@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.
Ah, I wasn't aware of this.
Context:Suet got the following error when she tried powering up a 64bit VM, a couple of months ago:
"This virtual machine is configured for 64-bit guest operating systems. However, 64-bit operation is not possible. This host does not support Intel VT-x. For more detailed information, see http://vmware.com/info?id=152." [The graphics problem was something different]
I guessed that pointing her at the 32bit Ubuntu iso would be easier than making BIOS changes (assuming her processor does support VT-x, but that it's disabled in BIOS).
Exactly, see my other answer :)
Florian: do you think the problem is related to 32bit-ness? If so, Suet can bring her laptop to Huxley or WPL some time this week and we'll go the 64bit route.
I'm not sure, I suspect not, but then I have no experience on 32bit systems (last time I used a 32bit system was 2009). Florian
Andrew
Florian
> Suet
participants (2)
-
Andrew McRae
-
Florian Rathgeber