Re: [OMPI users] Linker errors in Fedora 34 Docker container

[Jeff Squyres (jsquyres) via users]

John --

Can you supply all the information requested here:

https://www.open-mpi.org/community/help/

Thanks.


On May 25, 2021, at 5:44 PM, John Haiducek via users 
mailto:users@lists.open-mpi.org>> wrote:

Hi,

When attempting to build OpenMPI in a Fedora 34 Docker image I get the 
following linker errors:


#22 77.36 make[2]: Entering directory '/build/openmpi-4.1.1/opal/tools/wrappers'
#22 77.37   CC   opal_wrapper.o
#22 77.67   CCLD opal_wrapper
#22 77.81 /usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference 
to `opal_util_keyval_yytext'
#22 77.81 /usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference 
to `opal_util_keyval_yyin'
#22 77.81 /usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference 
to `opal_util_keyval_yylineno'
#22 77.81 /usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference 
to `opal_util_keyval_yynewlines'
#22 77.81 /usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference 
to `opal_util_keyval_yylex'
#22 77.81 /usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference 
to `opal_util_keyval_parse_done'
#22 77.81 /usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference 
to `opal_util_keyval_yylex_destroy'
#22 77.81 /usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference 
to `opal_util_keyval_init_buffer'
#22 77.81 collect2: error: ld returned 1 exit status

My configure command is just ./configure --prefix=/usr/local/openmpi.

I also tried ./configure --prefix=/usr/local/openmpi --disable-silent-rules 
--enable-builtin-atomics --with-hwloc=/usr --with-libevent=external 
--with-pmix=external --with-valgrind (similar to what is in the Fedora spec 
file for OpenMPI) but that produces the same errors.

Is there a third-party library I need to install or an additional configure 
option I can set that will fix these?

John


--
Jeff Squyres
jsquy...@cisco.com

Re: [OMPI users] [EXTERNAL] Linker errors in Fedora 34 Docker container

[Gilles Gouaillardet via users]

Howard,



I have a recollection of a similar issue that only occurs with the 
latest flex (that requires its own library to be passed to the linker).

I cannot remember if this was a flex packaging issue, or if we ended up 
recommending to downgrade flex to

a known to work version.



The issue should not happen if building from an official tarball though.



Cheers,



Gilles

- Original Message -

Hi John,

 

I don’t think an external dependency is going to fix this.

 

In your build area, do you see any .lo files in

 

opal/util/keyval

 

?

 

Which compiler are you using?

 

Also, are you building from the tarballs at 
https://www.open-mpi.org/software/ompi/v4.1/
 ?

 

Howard

 

From: users  on behalf of John 
Haiducek via users 
Reply-To: Open MPI Users 
Date: Tuesday, May 25, 2021 at 3:49 PM
To: "users@lists.open-mpi.org" 
Cc: John Haiducek 
Subject: [EXTERNAL] [OMPI users] Linker errors in Fedora 34 Docker 
container

 

Hi,

 

When attempting to build OpenMPI in a Fedora 34 Docker image I get the 
following linker errors:

 

#22 77.36 make[2]: Entering directory '/build/openmpi-4.1.1/opal/tools/
wrappers'
#22 77.37   CC   opal_wrapper.o
#22 77.67   CCLD opal_wrapper
#22 77.81 /usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined 
reference to `opal_util_keyval_yytext'
#22 77.81 /usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined 
reference to `opal_util_keyval_yyin'
#22 77.81 /usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined 
reference to `opal_util_keyval_yylineno'
#22 77.81 /usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined 
reference to `opal_util_keyval_yynewlines'
#22 77.81 /usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined 
reference to `opal_util_keyval_yylex'
#22 77.81 /usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined 
reference to `opal_util_keyval_parse_done'
#22 77.81 /usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined 
reference to `opal_util_keyval_yylex_destroy'
#22 77.81 /usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined 
reference to `opal_util_keyval_init_buffer'
#22 77.81 collect2: error: ld returned 1 exit status
My configure command is just ./configure --prefix=/usr/local/openmpi.

I also tried ./configure --prefix=/usr/local/openmpi --disable-silent-
rules --enable-builtin-atomics --with-hwloc=/usr --with-libevent=
external --with-pmix=external --with-valgrind (similar to what is in the 
Fedora spec file for OpenMPI) but that produces the same errors.

 

Is there a third-party library I need to install or an additional 
configure option I can set that will fix these?

 

John
 

Re: [OMPI users] [EXTERNAL] Linker errors in Fedora 34 Docker container

[Pritchard Jr., Howard via users]

Hi John,

I don’t think an external dependency is going to fix this.

In your build area, do you see any .lo files in

opal/util/keyval

?

Which compiler are you using?

Also, are you building from the tarballs at 
https://www.open-mpi.org/software/ompi/v4.1/ ?

Howard

From: users  on behalf of John Haiducek via 
users 
Reply-To: Open MPI Users 
Date: Tuesday, May 25, 2021 at 3:49 PM
To: "users@lists.open-mpi.org" 
Cc: John Haiducek 
Subject: [EXTERNAL] [OMPI users] Linker errors in Fedora 34 Docker container

Hi,

When attempting to build OpenMPI in a Fedora 34 Docker image I get the 
following linker errors:


#22 77.36 make[2]: Entering directory '/build/openmpi-4.1.1/opal/tools/wrappers'

#22 77.37   CC   opal_wrapper.o

#22 77.67   CCLD opal_wrapper

#22 77.81 /usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference 
to `opal_util_keyval_yytext'

#22 77.81 /usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference 
to `opal_util_keyval_yyin'

#22 77.81 /usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference 
to `opal_util_keyval_yylineno'

#22 77.81 /usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference 
to `opal_util_keyval_yynewlines'

#22 77.81 /usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference 
to `opal_util_keyval_yylex'

#22 77.81 /usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference 
to `opal_util_keyval_parse_done'

#22 77.81 /usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference 
to `opal_util_keyval_yylex_destroy'

#22 77.81 /usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference 
to `opal_util_keyval_init_buffer'

#22 77.81 collect2: error: ld returned 1 exit status
My configure command is just ./configure --prefix=/usr/local/openmpi.
I also tried ./configure --prefix=/usr/local/openmpi --disable-silent-rules 
--enable-builtin-atomics --with-hwloc=/usr --with-libevent=external 
--with-pmix=external --with-valgrind (similar to what is in the Fedora spec 
file for OpenMPI) but that produces the same errors.

Is there a third-party library I need to install or an additional configure 
option I can set that will fix these?

John

[OMPI users] Linker errors in Fedora 34 Docker container

[John Haiducek via users]

Hi,

When attempting to build OpenMPI in a Fedora 34 Docker image I get the 
following linker errors:

#22 77.36 make[2]: Entering directory '/build/openmpi-4.1.1/opal/tools/wrappers'
#22 77.37   CC   opal_wrapper.o
#22 77.67   CCLD opal_wrapper
#22 77.81 /usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference 
to `opal_util_keyval_yytext'
#22 77.81 /usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference 
to `opal_util_keyval_yyin'
#22 77.81 /usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference 
to `opal_util_keyval_yylineno'
#22 77.81 /usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference 
to `opal_util_keyval_yynewlines'
#22 77.81 /usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference 
to `opal_util_keyval_yylex'
#22 77.81 /usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference 
to `opal_util_keyval_parse_done'
#22 77.81 /usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference 
to `opal_util_keyval_yylex_destroy'
#22 77.81 /usr/bin/ld: ../../../opal/.libs/libopen-pal.so: undefined reference 
to `opal_util_keyval_init_buffer'
#22 77.81 collect2: error: ld returned 1 exit status
My configure command is just ./configure --prefix=/usr/local/openmpi.

I also tried ./configure --prefix=/usr/local/openmpi --disable-silent-rules 
--enable-builtin-atomics --with-hwloc=/usr --with-libevent=external 
--with-pmix=external --with-valgrind (similar to what is in the Fedora spec 
file for OpenMPI) but that produces the same errors.


Is there a third-party library I need to install or an additional configure 
option I can set that will fix these?

John