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Problems with mpich #853

Closed mpichbot closed 7 years ago

mpichbot commented 7 years ago

Originally by "David Lyder" david.lyder@gov.ab.ca on 2009-09-03 12:40:02 -0500


Hi!
I have been trying to get mpich-1.2.7p1 installed on my workstation (HP
xw8600 with 8 intel processors) and I have been having some difficulty.
I would like to be able to use the CMAQ and SMOKE modelling programs for
work related to photochemical air modelling and they use mpich in their
processing.
I have have used a cshrc file to set up my environmental variables.
Under these conditions I am trying to install mpich with the following
sequence:
1. From the directory with the mpich source code:
./configure --prefix=/model2/cmaq4.6/lib/mpich-1.2.7p1 |& tee config.log

This seems to work correctly on the basis of the info sent to the screen
but there are warnings generated that are caught in the log file
specifying there were problems with undefined references to gethrtime,
clock_gettime and clock_getres. Also, the configure file could not find
/sys/sockio.h
2. Next, I ran:
make |& tee make.log
On the screen this time there were errors reported regarding linking an
animation library and graphics library and these links failed.
3. Finally, I ran:
make install |& tee make_install.log
In this case the make process died right away and complained that tarch
was the same and would not be moved.
Note: When I restart the machine and go through the above steps all the
way through make install does generate a mpichinstall.o file but I don't
trust it since the errors mentioned in steps 1 and 2 still persisted.
I have attached all of the relevant files below.
Any thoughts, comments, opinions as to how to correct this would be
greatly appreciated.
Thanks,

David A. Lyder, Ph.D., E.I.T
Air Emissions Specialist, Air Policy Branch
Environmental Assurance Division
Alberta Environment
11th Floor, Baker Centre
10025-106 Street, Edmonton, Alberta T5J 1G4
Phone: (780) 644-8693 Fax: (780) 644-8946

[attachment:"untitled-part.html"]

mpichbot commented 7 years ago

Originally by david.lyder@gov.ab.ca on 2009-09-03 12:40:02 -0500

This message has 1 attachment(s)

mpichbot commented 7 years ago

Originally by david.lyder@gov.ab.ca on 2009-09-03 12:40:02 -0500

Attachment added: untitled-part.html (3.5 KiB) Added by email2trac

mpichbot commented 7 years ago

Originally by chan on 2009-09-03 14:03:52 -0500

MPICH-1, 1.2.7p1, is very old and its development has been stopped. The latest MPICH, MPICH2-1.1.1p1, is where we put our effort and it is a lot more robust especially for new hardware. Could you try MPICH2 instead ?

A.Chan

mpichbot commented 7 years ago

Originally by david.lyder@gov.ab.ca on 2009-09-03 14:20:02 -0500


Hi!

Thanks for your note. Is MPICH2-1.1.1p1 the most stable version?

Thanks,

David

-----Original Message-----
From: mpich2 [mailto:mpich2-maint@mcs.anl.gov]
Sent: Thursday, September 03, 2009 1:04 PM
Subject: Re: [mpich2-maint] #853: Problems with mpich

#853: Problems with mpich
---------------------------------------------------+--------------------
---------------------------------------------------+----
 Reporter:  "David Lyder" <david.lyder@...>          |       Owner:
     Type:  defect                                 |      Status:  new
 Priority:  major                                  |   Milestone:
Component:  mpich2                                 |    Keywords:
---------------------------------------------------+--------------------
---------------------------------------------------+----

Comment(by chan):

 MPICH-1, 1.2.7p1, is very old and its development has been stopped.
 The latest MPICH, MPICH2-1.1.1p1, is where we put our effort and it  is
a lot more robust especially for new hardware.
 Could you try MPICH2 instead ?

 A.Chan

--
Ticket URL:
<http://trac.mcs.anl.gov/projects/mpich2/ticket/853#comment:3>
mpich2 <http://www.mcs.anl.gov/research/projects/mpich2>
How to edit this ticket:
http://wiki.mcs.anl.gov/mpich2/index.php/Creating_New_Bug_Tickets
mpichbot commented 7 years ago

Originally by david.lyder@gov.ab.ca on 2009-09-03 15:20:02 -0500


Hi!

I have installed mpich2-1.1.1p1 and didn't get very far. I have attached
the output from the configuration step. I have no idea where to go from
here.

Thank you,

David

-----Original Message-----
From: mpich2 [mailto:mpich2-maint@mcs.anl.gov]
Sent: Thursday, September 03, 2009 1:04 PM
Subject: Re: [mpich2-maint] #853: Problems with mpich

#853: Problems with mpich
---------------------------------------------------+--------------------
---------------------------------------------------+----
 Reporter:  "David Lyder" <david.lyder@...>          |       Owner:
     Type:  defect                                 |      Status:  new
 Priority:  major                                  |   Milestone:
Component:  mpich2                                 |    Keywords:
---------------------------------------------------+--------------------
---------------------------------------------------+----

Comment(by chan):

 MPICH-1, 1.2.7p1, is very old and its development has been stopped.
 The latest MPICH, MPICH2-1.1.1p1, is where we put our effort and it  is
a lot more robust especially for new hardware.
 Could you try MPICH2 instead ?

 A.Chan

--
Ticket URL:
<http://trac.mcs.anl.gov/projects/mpich2/ticket/853#comment:3>
mpich2 <http://www.mcs.anl.gov/research/projects/mpich2>
How to edit this ticket:
http://wiki.mcs.anl.gov/mpich2/index.php/Creating_New_Bug_Tickets

[attachment:"config.log"]

mpichbot commented 7 years ago

Originally by david.lyder@gov.ab.ca on 2009-09-03 15:20:02 -0500

Attachment added: config.log (344.7 KiB) Added by email2trac

mpichbot commented 7 years ago

Originally by chan on 2009-09-03 15:40:55 -0500

I should have paid more attention to your 1st email. You should NOT pipe the configure output to config.log which is a logging file generated automatically by configure. As in MPICH2's README (which you should read), other file names like c.txt should be used for configure output. (also most email clients would recognize .txt an ascii file (easier for us)).

CPP means C PreProcessor not C++. C++ compiler should be specified through env variable CXX. Flags for C+ should be specified through CXXFLAGS. That is the likely cause of your error.

Can you rerun configure (be sure to do a "make distclean" first) and send us the configure and/or make outputs (as stated in README) if there is still error.

A.Chan

mpichbot commented 7 years ago

Originally by thakur on 2009-09-03 15:43:45 -0500

Can you unset CPPFLAGS and use CXXFLAGS instead?

We don't test with the PG compilers much. Can you try using gcc and g++ as the C and C++ compilers, and use pgf90 for Fortran. Set the env variables CC, CXX, F77, and F90 to the names of the compilers.

Rajeev

mpichbot commented 7 years ago

Originally by david.lyder@gov.ab.ca on 2009-09-03 16:40:01 -0500

Attachment added: make_install.txt (0.4 KiB) Added by email2trac

mpichbot commented 7 years ago

Originally by david.lyder@gov.ab.ca on 2009-09-03 16:40:01 -0500

Attachment added: make.txt (376.0 KiB) Added by email2trac

mpichbot commented 7 years ago

Originally by david.lyder@gov.ab.ca on 2009-09-03 16:40:01 -0500

Attachment added: cshrc (1.1 KiB) Added by email2trac

mpichbot commented 7 years ago

Originally by david.lyder@gov.ab.ca on 2009-09-03 16:40:01 -0500

Attachment added: congfig.txt (32.2 KiB) Added by email2trac

mpichbot commented 7 years ago

Originally by david.lyder@gov.ab.ca on 2009-09-03 16:40:01 -0500


Hi Jajeev,

Thank you for your note. I have made the changes and configure seemed to
work. However, make still generated warnings and make install did not
work. I have attached the relevant files.

Thank you,

David

-----Original Message-----
From: mpich2 [mailto:mpich2-maint@mcs.anl.gov]
Sent: Thursday, September 03, 2009 2:44 PM
Subject: Re: [mpich2-maint] #853: Problems with mpich

#853: Problems with mpich
---------------------------------------------------+--------------------
---------------------------------------------------+----
 Reporter:  "David Lyder" <david.lyder@...>          |       Owner:
     Type:  defect                                 |      Status:  new
 Priority:  major                                  |   Milestone:
Component:  mpich2                                 |    Keywords:
---------------------------------------------------+--------------------
---------------------------------------------------+----

Comment(by thakur):

 Can you unset CPPFLAGS and use CXXFLAGS instead?

 We don't test with the PG compilers much. Can you try using gcc and g++
as  the C and C++ compilers, and use pgf90 for Fortran. Set the env
variables  CC, CXX, F77, and F90 to the names of the compilers.

 Rajeev

--
Ticket URL:
<http://trac.mcs.anl.gov/projects/mpich2/ticket/853#comment:7>
mpich2 <http://www.mcs.anl.gov/research/projects/mpich2>
How to edit this ticket:
http://wiki.mcs.anl.gov/mpich2/index.php/Creating_New_Bug_Tickets

[attachment:"make_install.txt"]

[attachment:"congfig.txt"]

[attachment:"cshrc"]

[attachment:"make.txt"]

mpichbot commented 7 years ago

Originally by thakur on 2009-09-03 17:42:24 -0500

This make output is from MPICH1 1.2.7. Can you try MPICH2?

mpichbot commented 7 years ago

Originally by thakur@mcs.anl.gov on 2009-09-03 17:50:01 -0500


This make output is from MPICH1 1.2.7. Can you try MPICH2?
mpichbot commented 7 years ago

Originally by david.lyder@gov.ab.ca on 2009-09-03 17:50:04 -0500


Thanks for your note.

I have tried mpich2 with even less success - the configure step failed
completely. I have already sent the results from attempting to install
mpich2-1.1.1p1 in an earlier e-mail.

David

-----Original Message-----
From: mpich2 [mailto:mpich2-maint@mcs.anl.gov]
Sent: Thursday, September 03, 2009 4:42 PM
Subject: Re: [mpich2-maint] #853: Problems with mpich

#853: Problems with mpich
---------------------------------------------------+--------------------
---------------------------------------------------+----
 Reporter:  "David Lyder" <david.lyder@...>          |       Owner:
     Type:  defect                                 |      Status:  new
 Priority:  major                                  |   Milestone:
Component:  mpich2                                 |    Keywords:
---------------------------------------------------+--------------------
---------------------------------------------------+----

Comment(by thakur):

 This make output is from MPICH1 1.2.7. Can you try MPICH2?

--
Ticket URL:
<http://trac.mcs.anl.gov/projects/mpich2/ticket/853#comment:9>
mpich2 <http://www.mcs.anl.gov/research/projects/mpich2>
How to edit this ticket:
http://wiki.mcs.anl.gov/mpich2/index.php/Creating_New_Bug_Tickets
mpichbot commented 7 years ago

Originally by thakur on 2009-09-03 19:32:34 -0500

My earlier note (reproduced below) was for MPICH2. We don't support MPICH-1 any more.

Can you unset CPPFLAGS and use CXXFLAGS instead? (before configure)

We don't test with the PG compilers much. Can you try using gcc and g++ as the C and C++ compilers, and use pgf90 for Fortran. Set the env

variables CC, CXX, F77, and F90 to the names of the compilers.

mpichbot commented 7 years ago

Originally by david.lyder@gov.ab.ca on 2009-09-04 14:30:02 -0500


Hi!

First of all - thank you for the help with this, I really do appreciate
it.

I have switched to mpich2 and changed the flags in the cshrc file as
suggested. mpich2 certainly seems better behaved and I think it is not
too far from running now. However, there do still appear to be some
problems.

When running "configure" I do see a couple of warning messages coming to
the screen related to atomic primitives and the program ignoring
datarootdir but it seems to end properly. Looking inside of config.log
suggests there are errors that do need to be taken care of.

When running "make" there are plenty of warning and a failure to link to
the graphics/animation libraries. The pathing to XR11 seems correct -
the libraries do seem to be there.

Whne running "make install" the make fails pretty quickly with an error
that make install doesn't want to install a library that already exists.

I have attached all of the relevant files.

Any and all suggestions are greatly appreciated.

Cheers,

David

-----Original Message-----
From: mpich2 [mailto:mpich2-maint@mcs.anl.gov]
Sent: Thursday, September 03, 2009 6:33 PM
Subject: Re: [mpich2-maint] #853: Problems with mpich

#853: Problems with mpich
---------------------------------------------------+--------------------
---------------------------------------------------+----
 Reporter:  "David Lyder" <david.lyder@...>          |       Owner:
     Type:  defect                                 |      Status:  new
 Priority:  major                                  |   Milestone:
Component:  mpich2                                 |    Keywords:
---------------------------------------------------+--------------------
---------------------------------------------------+----

Comment(by thakur):

 My earlier note (reproduced below) was for MPICH2. We don't support
 MPICH-1 any more.

 ----
 Can you unset CPPFLAGS and use CXXFLAGS instead? (before configure)

  We don't test with the PG compilers much. Can you try using gcc and
g++  as  the C and C++ compilers, and use pgf90 for Fortran. Set the env
variables  CC, CXX, F77, and F90 to the names of the compilers.
 ------

--
Ticket URL:
<http://trac.mcs.anl.gov/projects/mpich2/ticket/853#comment:12>
mpich2 <http://www.mcs.anl.gov/research/projects/mpich2>
How to edit this ticket:
http://wiki.mcs.anl.gov/mpich2/index.php/Creating_New_Bug_Tickets

[attachment:"make_install-1.txt"]

[attachment:"config-1.log"]

[attachment:"config.txt"]

[attachment:"cshrc-1"]

[attachment:"make-1.txt"]

mpichbot commented 7 years ago

Originally by david.lyder@gov.ab.ca on 2009-09-04 14:30:06 -0500

Attachment added: make_install-1.txt (2.3 KiB) Added by email2trac

mpichbot commented 7 years ago

Originally by david.lyder@gov.ab.ca on 2009-09-04 14:30:06 -0500

Attachment added: config-1.log (351.7 KiB) Added by email2trac

mpichbot commented 7 years ago

Originally by david.lyder@gov.ab.ca on 2009-09-04 14:30:06 -0500

Attachment added: config.txt (104.3 KiB) Added by email2trac

mpichbot commented 7 years ago

Originally by david.lyder@gov.ab.ca on 2009-09-04 14:30:06 -0500

Attachment added: make-1.txt (197.4 KiB) Added by email2trac

mpichbot commented 7 years ago

Originally by david.lyder@gov.ab.ca on 2009-09-04 14:30:06 -0500

Attachment added: cshrc-1 (1.1 KiB) Added by email2trac

mpichbot commented 7 years ago

Originally by chan on 2009-09-04 16:52:04 -0500

"make install" failed is most likely due to you set mpich2 install directory the same as mpich2 source directory (where you untar mpich2-xxx.tar.gz to) and also you are doing an inpath build. Set --prefix to some other directory and redo configure/make/make install and be sure to do "make distclean" first.