[OMPI users] Debug build of v3.0.1 tarball

Discussion:

Moody, Adam T.

2018-05-03 21:00:47 UTC

Hello Open MPI team,

I'm looking for the recommended way to produce a debug build of Open MPI v3.0.1 that compiles with â-g -O0â so that I get accurate debug info under a debugger.

So far, I've gone through the following sequence. I started with CFLAGS="-g -O0" on make:

shell$ ./configure --prefix=$installdir --disable-silent-rules \

--disable-new-dtags --enable-mpi-cxx --enable-cxx-exceptions --with-pmi

shell$ make -j CFLAGS="-g -O0" VERBOSE=1

That led to the following error:

In file included from ../../../../opal/util/arch.h:26:0,

from btl_openib.h:43,

from btl_openib_component.c:79:

btl_openib_component.c: In function 'progress_pending_frags_wqe':

btl_openib_component.c:3351:29: error: 'opal_list_item_t' has no member named 'opal_list_item_refcount'

assert(0 == frag->opal_list_item_refcount);

^

make[2]: *** [btl_openib_component.lo] Error 1

make[2]: *** Waiting for unfinished jobs....

make[2]: Leaving directory `.../openmpi-3.0.1/opal/mca/btl/openib'

So it seems the assert is referring to a field structure that is protected by a debug flag. I then added --enable-debug to configure, which led to:

make[2]: Entering directory `.../openmpi-3.0.1/opal/tools/wrappers'

CC opal_wrapper.o

GENERATE opal_wrapper.1

CCLD opal_wrapper

../../../opal/.libs/libopen-pal.so: undefined reference to `pthread_atfork'

collect2: error: ld returned 1 exit status

make[2]: *** [opal_wrapper] Error 1

make[2]: Leaving directory `.../openmpi-3.0.1/opal/tools/wrappers'

Finally, if I also add LDFLAGS="-lpthread" to make, I get a build:

shell$ ./configure --prefix=$installdir --enable-debug --disable-silent-rules \

--disable-new-dtags --enable-mpi-cxx --enable-cxx-exceptions --with-pmi

shell$ make -j CFLAGS="-g -O0" LDFLAGS="-lpthread" VERBOSE=1

Am I doing this correctly?

Is there a pointer to the configure/make flags for this?

I did find this page that describes the developer build from a git clone, but that seemed a bit overkill since I am looking for a debug build from the distribution tarball instead of the git clone (avoid the autotools nightmare):

https://www.open-mpi.org/source/building.php

Thanks.

-Adam

Howard Pritchard

2018-05-04 14:22:28 UTC

Permalink

Hi Adam,

Did you try using the --enable-debug configure option along with your
CFLAGS options?
You may want to see if that simplifies your build.

In any case, we'll fix the problems you found.

Howard

Post by Moody, Adam T.
Hello Open MPI team,
I'm looking for the recommended way to produce a debug build of Open MPI
v3.0.1 that compiles with â-g -O0â so that I get accurate debug info under
a debugger.
shell$ ./configure --prefix=$installdir --disable-silent-rules \
--disable-new-dtags --enable-mpi-cxx --enable-cxx-exceptions --with-pmi
shell$ make -j CFLAGS="-g -O0" VERBOSE=1
In file included from ../../../../opal/util/arch.h:26:0,
from btl_openib.h:43,
btl_openib_component.c:3351:29: error: 'opal_list_item_t' has no member named 'opal_list_item_refcount'
assert(0 == frag->opal_list_item_refcount);
^
make[2]: *** [btl_openib_component.lo] Error 1
make[2]: *** Waiting for unfinished jobs....
make[2]: Leaving directory `.../openmpi-3.0.1/opal/mca/btl/openib'
So it seems the assert is referring to a field structure that is protected
make[2]: Entering directory `.../openmpi-3.0.1/opal/tools/wrappers'
CC opal_wrapper.o
GENERATE opal_wrapper.1
CCLD opal_wrapper
../../../opal/.libs/libopen-pal.so: undefined reference to `pthread_atfork'
collect2: error: ld returned 1 exit status
make[2]: *** [opal_wrapper] Error 1
make[2]: Leaving directory `.../openmpi-3.0.1/opal/tools/wrappers'
shell$ ./configure --prefix=$installdir --enable-debug --disable-silent-rules \
--disable-new-dtags --enable-mpi-cxx --enable-cxx-exceptions --with-pmi
shell$ make -j CFLAGS="-g -O0" LDFLAGS="-lpthread" VERBOSE=1
Am I doing this correctly?
Is there a pointer to the configure/make flags for this?
I did find this page that describes the developer build from a git clone,
but that seemed a bit overkill since I am looking for a debug build from
the distribution tarball instead of the git clone (avoid the autotools
https://www.open-mpi.org/source/building.php
Thanks.
-Adam
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users

Howard Pritchard

2018-05-04 14:42:41 UTC

Permalink

HI Adam,

Sorry didn't notice you did try the --enable-debug flag. That should not
have
led to the link error building the opal dso. Did you do a make clean after
rerunning configure?

Howard

Post by Howard Pritchard
Hi Adam,
Did you try using the --enable-debug configure option along with your
CFLAGS options?
You may want to see if that simplifies your build.
In any case, we'll fix the problems you found.
Howard

Post by Moody, Adam T.
Hello Open MPI team,
I'm looking for the recommended way to produce a debug build of Open MPI
v3.0.1 that compiles with â-g -O0â so that I get accurate debug info under
a debugger.
So far, I've gone through the following sequence. I started with
shell$ ./configure --prefix=$installdir --disable-silent-rules \
--disable-new-dtags --enable-mpi-cxx --enable-cxx-exceptions --with-pmi
shell$ make -j CFLAGS="-g -O0" VERBOSE=1
In file included from ../../../../opal/util/arch.h:26:0,
from btl_openib.h:43,
btl_openib_component.c:3351:29: error: 'opal_list_item_t' has no member named 'opal_list_item_refcount'
assert(0 == frag->opal_list_item_refcount);
^
make[2]: *** [btl_openib_component.lo] Error 1
make[2]: *** Waiting for unfinished jobs....
make[2]: Leaving directory `.../openmpi-3.0.1/opal/mca/btl/openib'
So it seems the assert is referring to a field structure that is
protected by a debug flag. I then added --enable-debug to configure, which
make[2]: Entering directory `.../openmpi-3.0.1/opal/tools/wrappers'
CC opal_wrapper.o
GENERATE opal_wrapper.1
CCLD opal_wrapper
../../../opal/.libs/libopen-pal.so: undefined reference to `pthread_atfork'
collect2: error: ld returned 1 exit status
make[2]: *** [opal_wrapper] Error 1
make[2]: Leaving directory `.../openmpi-3.0.1/opal/tools/wrappers'
shell$ ./configure --prefix=$installdir --enable-debug --disable-silent-rules \
--disable-new-dtags --enable-mpi-cxx --enable-cxx-exceptions --with-pmi
shell$ make -j CFLAGS="-g -O0" LDFLAGS="-lpthread" VERBOSE=1
Am I doing this correctly?
Is there a pointer to the configure/make flags for this?
I did find this page that describes the developer build from a git clone,
but that seemed a bit overkill since I am looking for a debug build from
the distribution tarball instead of the git clone (avoid the autotools
https://www.open-mpi.org/source/building.php
Thanks.
-Adam
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users

Moody, Adam T.

2018-05-04 18:09:31 UTC

Permalink

Hi Howard,
I do have a make clean after the configure. To be extra safe, Iâm now also deleting the source directory and untarring for each build to make sure I have a clean starting point.

I do get a successful build if I add --enable-debug to configure and then do a simple make that has no CFLAGS or LDFLAGS:

make -j VERBOSE=1

So thatâs good. However, looking at the compile lines that were used, I see a -g but no -O0. Iâm trying to force the -g -O0, because our debuggers show the best info at that optimization level.

If I then also add a CFLAGS=â-g -O0â to my make command, I see the â-g -O0â in the compile lines, but then the pthread link error shows up:

make -j CFLAGS=â-g -O0â VERBOSE=1

CC opal_wrapper.o
GENERATE opal_wrapper.1
CCLD opal_wrapper
../../../opal/.libs/libopen-pal.so: undefined reference to `pthread_atfork'
collect2: error: ld returned 1 exit status
make[2]: *** [opal_wrapper] Error 1

Also setting LDFLAGS fixes that up. Just wondering whether Iâm going about it the right way in trying to get -g -O0 in the build.

Thanks for your help,
-Adam

From: users <users-***@lists.open-mpi.org> on behalf of Howard Pritchard <***@gmail.com>
Reply-To: Open MPI Users <***@lists.open-mpi.org>
Date: Friday, May 4, 2018 at 7:46 AM
To: Open MPI Users <***@lists.open-mpi.org>
Subject: Re: [OMPI users] Debug build of v3.0.1 tarball

HI Adam,

Sorry didn't notice you did try the --enable-debug flag. That should not have
led to the link error building the opal dso. Did you do a make clean after
rerunning configure?

Howard

2018-05-04 8:22 GMT-06:00 Howard Pritchard <***@gmail.com<mailto:***@gmail.com>>:
Hi Adam,

Did you try using the --enable-debug configure option along with your CFLAGS options?
You may want to see if that simplifies your build.

In any case, we'll fix the problems you found.

Howard

2018-05-03 15:00 GMT-06:00 Moody, Adam T. <***@llnl.gov<mailto:***@llnl.gov>>:

Hello Open MPI team,

I'm looking for the recommended way to produce a debug build of Open MPI v3.0.1 that compiles with â-g -O0â so that I get accurate debug info under a debugger.

So far, I've gone through the following sequence. I started with CFLAGS="-g -O0" on make:

shell$ ./configure --prefix=$installdir --disable-silent-rules \

--disable-new-dtags --enable-mpi-cxx --enable-cxx-exceptions --with-pmi

shell$ make -j CFLAGS="-g -O0" VERBOSE=1

That led to the following error:

In file included from ../../../../opal/util/arch.h:26:0,

from btl_openib.h:43,

from btl_openib_component.c:79:

btl_openib_component.c: In function 'progress_pending_frags_wqe':

btl_openib_component.c:3351:29: error: 'opal_list_item_t' has no member named 'opal_list_item_refcount'

assert(0 == frag->opal_list_item_refcount);

^

make[2]: *** [btl_openib_component.lo] Error 1

make[2]: *** Waiting for unfinished jobs....

make[2]: Leaving directory `.../openmpi-3.0.1/opal/mca/btl/openib'

So it seems the assert is referring to a field structure that is protected by a debug flag. I then added --enable-debug to configure, which led to:

make[2]: Entering directory `.../openmpi-3.0.1/opal/tools/wrappers'

CC opal_wrapper.o

GENERATE opal_wrapper.1

CCLD opal_wrapper

../../../opal/.libs/libopen-pal.so: undefined reference to `pthread_atfork'

collect2: error: ld returned 1 exit status

make[2]: *** [opal_wrapper] Error 1

make[2]: Leaving directory `.../openmpi-3.0.1/opal/tools/wrappers'

Finally, if I also add LDFLAGS="-lpthread" to make, I get a build:

shell$ ./configure --prefix=$installdir --enable-debug --disable-silent-rules \

--disable-new-dtags --enable-mpi-cxx --enable-cxx-exceptions --with-pmi

shell$ make -j CFLAGS="-g -O0" LDFLAGS="-lpthread" VERBOSE=1

Am I doing this correctly?

Is there a pointer to the configure/make flags for this?

I did find this page that describes the developer build from a git clone, but that seemed a bit overkill since I am looking for a debug build from the distribution tarball instead of the git clone (avoid the autotools nightmare):

https://www.open-mpi.org/source/building.php

Thanks.

-Adam

_______________________________________________
users mailing list
***@lists.open-mpi.org<mailto:***@lists.open-mpi.org>
https://lists.open-mpi.org/mailman/listinfo/users

Howard Pritchard

2018-05-04 20:07:31 UTC

Permalink

HI Adam,

I think you'll have better luck setting the CFLAGS on the configure line.

try

./configure CFLAGS="-g -O0" your other configury options.

Howard

Post by Moody, Adam T.
Hi Howard,
I do have a make clean after the configure. To be extra safe, Iâm now
also deleting the source directory and untarring for each build to make
sure I have a clean starting point.
I do get a successful build if I add --enable-debug to configure and then
make -j VERBOSE=1
So thatâs good. However, looking at the compile lines that were used, I
see a -g but no -O0. Iâm trying to force the -g -O0, because our debuggers
show the best info at that optimization level.
If I then also add a CFLAGS=â-g -O0â to my make command, I see the â-g
make -j CFLAGS=â-g -O0â VERBOSE=1
CC opal_wrapper.o
GENERATE opal_wrapper.1
CCLD opal_wrapper
../../../opal/.libs/libopen-pal.so: undefined reference to
`pthread_atfork'
collect2: error: ld returned 1 exit status
make[2]: *** [opal_wrapper] Error 1
Also setting LDFLAGS fixes that up. Just wondering whether Iâm going
about it the right way in trying to get -g -O0 in the build.
Thanks for your help,
-Adam
*Date: *Friday, May 4, 2018 at 7:46 AM
*Subject: *Re: [OMPI users] Debug build of v3.0.1 tarball
HI Adam,
Sorry didn't notice you did try the --enable-debug flag. That should not have
led to the link error building the opal dso. Did you do a make clean after
rerunning configure?
Howard
Hi Adam,
Did you try using the --enable-debug configure option along with your CFLAGS options?
You may want to see if that simplifies your build.
In any case, we'll fix the problems you found.
Howard
Hello Open MPI team,
I'm looking for the recommended way to produce a debug build of Open MPI
v3.0.1 that compiles with â-g -O0â so that I get accurate debug info under
a debugger.
shell$ ./configure --prefix=$installdir --disable-silent-rules \
--disable-new-dtags --enable-mpi-cxx --enable-cxx-exceptions --with-pmi
shell$ make -j CFLAGS="-g -O0" VERBOSE=1
In file included from ../../../../opal/util/arch.h:26:0,
from btl_openib.h:43,
btl_openib_component.c:3351:29: error: 'opal_list_item_t' has no member named 'opal_list_item_refcount'
assert(0 == frag->opal_list_item_refcount);
^
make[2]: *** [btl_openib_component.lo] Error 1
make[2]: *** Waiting for unfinished jobs....
make[2]: Leaving directory `.../openmpi-3.0.1/opal/mca/btl/openib'
So it seems the assert is referring to a field structure that is protected
make[2]: Entering directory `.../openmpi-3.0.1/opal/tools/wrappers'
CC opal_wrapper.o
GENERATE opal_wrapper.1
CCLD opal_wrapper
../../../opal/.libs/libopen-pal.so: undefined reference to `pthread_atfork'
collect2: error: ld returned 1 exit status
make[2]: *** [opal_wrapper] Error 1
make[2]: Leaving directory `.../openmpi-3.0.1/opal/tools/wrappers'
shell$ ./configure --prefix=$installdir --enable-debug --disable-silent-rules \
--disable-new-dtags --enable-mpi-cxx --enable-cxx-exceptions --with-pmi
shell$ make -j CFLAGS="-g -O0" LDFLAGS="-lpthread" VERBOSE=1
Am I doing this correctly?
Is there a pointer to the configure/make flags for this?
I did find this page that describes the developer build from a git clone,
but that seemed a bit overkill since I am looking for a debug build from
the distribution tarball instead of the git clone (avoid the autotools
https://www.open-mpi.org/source/building.php
Thanks.
-Adam
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users

Moody, Adam T.

2018-05-04 20:49:16 UTC

Permalink

Ah, yes. That worked. Thanks, Howard.
-Adam

From: users <users-***@lists.open-mpi.org> on behalf of Howard Pritchard <***@gmail.com>
Reply-To: Open MPI Users <***@lists.open-mpi.org>
Date: Friday, May 4, 2018 at 1:13 PM
To: Open MPI Users <***@lists.open-mpi.org>
Subject: Re: [OMPI users] Debug build of v3.0.1 tarball

HI Adam,

I think you'll have better luck setting the CFLAGS on the configure line.

try

./configure CFLAGS="-g -O0" your other configury options.

Howard

2018-05-04 12:09 GMT-06:00 Moody, Adam T. <***@llnl.gov<mailto:***@llnl.gov>>:
Hi Howard,
I do have a make clean after the configure. To be extra safe, Iâm now also deleting the source directory and untarring for each build to make sure I have a clean starting point.

I do get a successful build if I add --enable-debug to configure and then do a simple make that has no CFLAGS or LDFLAGS:

make -j VERBOSE=1

So thatâs good. However, looking at the compile lines that were used, I see a -g but no -O0. Iâm trying to force the -g -O0, because our debuggers show the best info at that optimization level.

If I then also add a CFLAGS=â-g -O0â to my make command, I see the â-g -O0â in the compile lines, but then the pthread link error shows up:

make -j CFLAGS=â-g -O0â VERBOSE=1

CC opal_wrapper.o
GENERATE opal_wrapper.1
CCLD opal_wrapper
../../../opal/.libs/libopen-pal.so: undefined reference to `pthread_atfork'
collect2: error: ld returned 1 exit status
make[2]: *** [opal_wrapper] Error 1

Also setting LDFLAGS fixes that up. Just wondering whether Iâm going about it the right way in trying to get -g -O0 in the build.

Thanks for your help,
-Adam

From: users <users-***@lists.open-mpi.org<mailto:users-***@lists.open-mpi.org>> on behalf of Howard Pritchard <***@gmail.com<mailto:***@gmail.com>>
Reply-To: Open MPI Users <***@lists.open-mpi.org<mailto:***@lists.open-mpi.org>>
Date: Friday, May 4, 2018 at 7:46 AM
To: Open MPI Users <***@lists.open-mpi.org<mailto:***@lists.open-mpi.org>>
Subject: Re: [OMPI users] Debug build of v3.0.1 tarball

HI Adam,

Sorry didn't notice you did try the --enable-debug flag. That should not have
led to the link error building the opal dso. Did you do a make clean after
rerunning configure?

Howard

2018-05-04 8:22 GMT-06:00 Howard Pritchard <***@gmail.com<mailto:***@gmail.com>>:
Hi Adam,

Did you try using the --enable-debug configure option along with your CFLAGS options?
You may want to see if that simplifies your build.

In any case, we'll fix the problems you found.

Howard

2018-05-03 15:00 GMT-06:00 Moody, Adam T. <***@llnl.gov<mailto:***@llnl.gov>>:

Hello Open MPI team,

I'm looking for the recommended way to produce a debug build of Open MPI v3.0.1 that compiles with â-g -O0â so that I get accurate debug info under a debugger.

So far, I've gone through the following sequence. I started with CFLAGS="-g -O0" on make:

shell$ ./configure --prefix=$installdir --disable-silent-rules \

--disable-new-dtags --enable-mpi-cxx --enable-cxx-exceptions --with-pmi

shell$ make -j CFLAGS="-g -O0" VERBOSE=1

That led to the following error:

In file included from ../../../../opal/util/arch.h:26:0,

from btl_openib.h:43,

from btl_openib_component.c:79:

btl_openib_component.c: In function 'progress_pending_frags_wqe':

btl_openib_component.c:3351:29: error: 'opal_list_item_t' has no member named 'opal_list_item_refcount'

assert(0 == frag->opal_list_item_refcount);

^

make[2]: *** [btl_openib_component.lo] Error 1

make[2]: *** Waiting for unfinished jobs....

make[2]: Leaving directory `.../openmpi-3.0.1/opal/mca/btl/openib'

So it seems the assert is referring to a field structure that is protected by a debug flag. I then added --enable-debug to configure, which led to:

make[2]: Entering directory `.../openmpi-3.0.1/opal/tools/wrappers'

CC opal_wrapper.o

GENERATE opal_wrapper.1

CCLD opal_wrapper

../../../opal/.libs/libopen-pal.so: undefined reference to `pthread_atfork'

collect2: error: ld returned 1 exit status

make[2]: *** [opal_wrapper] Error 1

make[2]: Leaving directory `.../openmpi-3.0.1/opal/tools/wrappers'

Finally, if I also add LDFLAGS="-lpthread" to make, I get a build:

shell$ ./configure --prefix=$installdir --enable-debug --disable-silent-rules \

--disable-new-dtags --enable-mpi-cxx --enable-cxx-exceptions --with-pmi

shell$ make -j CFLAGS="-g -O0" LDFLAGS="-lpthread" VERBOSE=1

Am I doing this correctly?

Is there a pointer to the configure/make flags for this?

I did find this page that describes the developer build from a git clone, but that seemed a bit overkill since I am looking for a debug build from the distribution tarball instead of the git clone (avoid the autotools nightmare):

https://www.open-mpi.org/source/building.php

Thanks.

-Adam

_______________________________________________
users mailing list
***@lists.open-mpi.org<mailto:***@lists.open-mpi.org>
https://lists.open-mpi.org/mailman/listinfo/users

_______________________________________________
users mailing list
***@lists.open-mpi.org<mailto:***@lists.open-mpi.org>
https://lists.open-mpi.org/mailman/listinfo/users