MPICH2-1.1 : make fails with undefined reference to 'pthread_create'

["Timothy S. Sliwinski" <tss06@…>]

Mpich2-maint,



            I am running a server for a proof-of-concept project built on
FreeBSD-7.2-Release. When I first ran configure, it told me that I did not
have python installed. I went back and installed the FreeBSD port of
python-2.6 and re-ran configure for mpich2-1.1. Configure ran successfully
and c.txt showed no alarming errors that I am aware of. However, now when I
attempt to run make, I receive the following error:



In Function 'HYDU_create_thread':

:undefined reference to 'pthread_create'

*** Error code 1



Stop in /tmp/tim/mpich2/src/pm/hydra/pm/pmiserv.

*** Error code 1



Stop in /tmp/tim/mpich2/src/pm/hydra/pm.

*** Error code 1



..etc. (rest of error in m.txt)



I am following the Quick Start instructions for now in the installer's
guide.



I did try to go back a version to mpich2-1.0.p1 which completed configure,
make, and make install, but while running "mpd &", it would complain about
depreciated calls in the python scripts and hang and I figured my python
version was too new for it so I tried mpich2-1.1 again with the same errors.




I have attached the make output (m.txt) using the VERBOSE=1 option and the
configure output (c.txt). Any help you can give in regards to my mpich2-1.1
make errors would be greatly appreciated!!



-Timothy Sliwinski

Florida State University Student

[Timothy S. Sliwinski]

Added by email2trac

[Timothy S. Sliwinski]

This message has 3 attachment(s)

[balaji]

Timothy,

The problem with newer python versions has been fixed for 1.1. I'm not certain what the exact problem with hydra is (which is calling the HYDU_create_thread stuff), but it looks like the pthread library is not being linked in to the hydra binaries correctly. Your system does seem to have pthreads on it as detected by configure (your c.txt has this information).

While we look into this there are a few options that you can try:

1. MPICH2 binary packages are distributed by FreeBSD. So unless you want to modify the MPICH2 source, you can just do a "pkg_add -r mpich2" to install it.

2. You can disable hydra, and just configure MPD by passing the configure option --with-pm=mpd.

Let us know if this works for you.

-- Pavan

[balaji]

Can you also send us your config.log and config.status from the top-level configure as well as from src/pm/hydra?

[Timothy S. Sliwinski]

Added by email2trac

[Timothy S. Sliwinski]

Balaji,

I have attached the top-level and /src/pm/hydra config.log and config.status
files for you to look over. They are named so you can easily tell which is
which.

In regards to your first reply, I am about to try the second suggestion and
will let you know what happens. In regards to the first suggestion, the
FreeBSD port actually gave me the same errors so that is why I downloaded
the tarball. I believed the port was broken, but it looks like something
else is the matter.

Hope the information I am giving is helping you out! Thanks for the
extra-speedy responses too!

-Timothy Sliwinski
Florida State University Student

-----Original Message-----
From: owner-mpich2-bugs@mcs.anl.gov [mailto:owner-mpich2-bugs@mcs.anl.gov]
On Behalf Of mpich2
Sent: Sunday, June 28, 2009 6:29 PM
To: undisclosed-recipients:
Subject: Re: [mpich2-maint] #686: MPICH2-1.1 : make fails with undefined
reference to 'pthread_create'

----------------------------------------------------+-----------------------
 Reporter:  "Timothy S. Sliwinski" <tss06@fsu.edu>  |        Owner:  balaji

     Type:  bug                                     |       Status:  new

 Priority:  blocker                                 |    Milestone:
mpich2-1.1.1
Component:  mpich2                                  |   Resolution:

 Keywords:                                          |
----------------------------------------------------+-----------------------


Comment (by balaji):

 Can you also send us your config.log and config.status from the top-level
 configure as well as from src/pm/hydra?

--
Ticket URL: <https://trac.mcs.anl.gov/projects/mpich2/ticket/686#comment:3>

[balaji]

Thanks. I've added a (potential) fix for this in r4843 in the svn. Can you try out this tarball and let us know if it works for you: http://www.mcs.anl.gov/research/projects/mpich2/downloads/tarballs/nightly/trunk/mpich2-trunk-r4843.tar.gz

[Timothy S. Sliwinski]

Added by email2trac

[Timothy S. Sliwinski]

Balaji,

I tested the tarball you sent and though the pthread_create problem seems to
have been solved, a new one has appeared... also in hydra during make.

Error Message:

In function 'plpa_api_probe_init':
/home/tim/libraries/mpich2-trunk-r4843/src/pm/hydra/utils/plpa/plpa_api_prob
e.c:35:
Error: '__NR_sched_getaffinity' undeclared (first use in this function)

/home/tim/libraries/mpich2-trunk-r4843/src/pm/hydra/utils/plpa/plpa_api_prob
e.c:42:
Error: '__NR_sched_setaffinity' undeclared (first use in this function)

...etc(more in r4843_m.txt)

I've attached the c.txt and m.txt (using VERBOSE=1) for you.

On a side note, the --with-pm=mpd option helped 'make' finish without error.
Will try make install, and testing of mpd later on.

If you need any more config files from the r4843 make, I'll get them to you
as soon as I can.

- Timothy Sliwinski
Florida State University Student





-----Original Message-----
From: owner-mpich2-bugs@mcs.anl.gov [mailto:owner-mpich2-bugs@mcs.anl.gov]
On Behalf Of mpich2
Sent: Sunday, June 28, 2009 8:02 PM
To: undisclosed-recipients:
Subject: Re: [mpich2-maint] #686: MPICH2-1.1 : make fails with undefined
reference to 'pthread_create'

----------------------------------------------------+-----------------------
 Reporter:  "Timothy S. Sliwinski" <tss06@fsu.edu>  |        Owner:  balaji

     Type:  bug                                     |       Status:  new

 Priority:  blocker                                 |    Milestone:
mpich2-1.1.1
Component:  mpich2                                  |   Resolution:

 Keywords:                                          |
----------------------------------------------------+-----------------------


Comment (by balaji):

 Thanks. I've added a (potential) fix for this in r4843 in the svn. Can you
 try out this tarball and let us know if it works for you:

http://www.mcs.anl.gov/research/projects/mpich2/downloads/tarballs/nightly/t
runk/mpich2-trunk-r4843.tar.gz

--
Ticket URL: <https://trac.mcs.anl.gov/projects/mpich2/ticket/686#comment:5>

[balaji]

Ah, the NR_sched_getaffinity was an experimental addition which should not have been enabled for anything other than linux. Clearly the configure in src/pm/hydra is not working as expected. Can you do two things:

1. Configure with --disable-hydra-procbind and see if there are any other problems.

2. Send me src/pm/hydra/config.log and src/pm/hydra/config.status so I can figure out why configure thinks NR_sched_getaffinity works on your system, when it shouldn't.

-- Pavan

[Timothy S. Sliwinski]

Balaji,

IT WORKS! I was able to configure, make, and make install with no problem.
Tested mpd, mpdtrace, mpiexec -n 1 hostname, and mpdallexit and no errors or
warnings. I did realize I can't test an mpd ring until I get my nodes
reconfigured, but that's my problem, not yours. Heh.

I am attaching the r4843 /src/pm/hydra/config.log and config.sys along with
the m.txt, c.txt, mi.txt, hydra's config.status, and hydra's config.log that
worked with the --disable-hydra-procbind in case they hold some more clues
into what went wrong (they are labeled with "working_").

I appreciate your help and if you need anything else to solve this for
future releases, please let me know!

-Timothy Sliwinski
Florida State University Student

-----Original Message-----
From: owner-mpich2-bugs@mcs.anl.gov [mailto:owner-mpich2-bugs@mcs.anl.gov]
On Behalf Of mpich2
Sent: Sunday, June 28, 2009 10:29 PM
To: undisclosed-recipients:
Subject: Re: [mpich2-maint] #686: MPICH2-1.1 : make fails with undefined
reference to 'pthread_create'

----------------------------------------------------+-----------------------
 Reporter:  "Timothy S. Sliwinski" <tss06@fsu.edu>  |        Owner:  balaji

     Type:  bug                                     |       Status:  new

 Priority:  blocker                                 |    Milestone:
mpich2-1.1.1
Component:  mpich2                                  |   Resolution:

 Keywords:                                          |
----------------------------------------------------+-----------------------


Comment (by balaji):

 Ah, the __NR_sched_getaffinity was an experimental addition which should
 not have been enabled for anything other than linux. Clearly the configure
 in src/pm/hydra is not working as expected. Can you do two things:

 1. Configure with --disable-hydra-procbind and see if there are any other
 problems.

 2. Send me src/pm/hydra/config.log and src/pm/hydra/config.status so I can
 figure out why configure thinks __NR_sched_getaffinity works on your
 system, when it shouldn't.

  -- Pavan

--
Ticket URL: <https://trac.mcs.anl.gov/projects/mpich2/ticket/686#comment:7>

[Timothy S. Sliwinski]

Added by email2trac

[balaji]

Great! Thanks for the logs. This problem has been fixed in the svn as of r4860 and will appear in the next release (mpich2-1.1.1, which should be out in a few weeks). Resolving this ticket.

Btw, it is still advisable for you to use the released version of mpich2, rather than an intermediate snapshot, as it is much better tested.

-- Pavan