port atlas fails to upgrade

[aranoya@…]

i got the following error while upgrading atlas

----
sudo port upgrade atlas
--->  Computing dependencies for atlas
--->  Building atlas
Error: org.macports.build for port atlas returned: command execution failed
Please see the log file for port atlas for details:
    /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/main.log
Error: Unable to upgrade port: 1
To report a bug, follow the instructions in the guide:
    http://guide.macports.org/#project.tickets

---

main.log is attached.

thanks

[aranoya@…]

log file

[aranoya@…]

vince@…

[mf2k (Frank Schima)]

In the future, please use WikiFormatting.

[cecilyen@…]

Cc Me!

[Veence (Vincent)]

This is a clear bug in clang/llvm-3.3. Try again with the new Portfile (r105312). If you still get the same error, you should report it to the clang/llvm developers.

[Veence (Vincent)]

I’ve disabled the vectorizing flags for clang3.3 in r105324. Please retry (everyone).

[Veence (Vincent)]

This is definitely a regression in clang. With clang-mp-3.3 r173279, compilation is fine:

/opt/local/bin/clang-mp-3.3 -c -DL2SIZE=4194304 -I/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/atlas-3.10.1/build/include -I/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/atlas-3.10.1/build/..//include -I/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/atlas-3.10.1/build/..//include/contrib -DAdd_ -DF77_INTEGER=int -DStringSunStyle -DATL_OS_OSX -DATL_ARCH_Corei2 -DATL_CPUMHZ=2300 -DATL_AVX -DATL_SSE3 -DATL_SSE2 -DATL_SSE1 -DATL_USE64BITS -DATL_GAS_x8664 -DATL_DYLIBS -DPentiumCPS=2300 -DATL_FULL_LAPACK -DATL_NCPU=4 -O3 -fomit-frame-pointer -fPIC -fvectorize -fslp-vectorize -march=native -mavx  /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/atlas-3.10.1/build/..//tune/blas/gemm/gmmsearch.c
In file included from /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/atlas-3.10.1/build/..//tune/blas/gemm/gmmsearch.c:34:
In file included from /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/atlas-3.10.1/build/..//include/atlas_mmtesttime.h:4:
/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/atlas-3.10.1/build/..//include/atlas_mmparse.h:1011:14: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
   while (ln = GetJoinedLines(fpin))
          ~~~^~~~~~~~~~~~~~~~~~~~~~
/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/atlas-3.10.1/build/..//include/atlas_mmparse.h:1011:14: note: place parentheses around the assignment to silence this warning
   while (ln = GetJoinedLines(fpin))
             ^
          (                        )
/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/atlas-3.10.1/build/..//include/atlas_mmparse.h:1011:14: note: use '==' to turn this assignment into an equality comparison
   while (ln = GetJoinedLines(fpin))
             ^
             ==
1 warning generated.
/opt/local/bin/clang-mp-3.3 -DL2SIZE=4194304 -I/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/atlas-3.10.1/build/include -I/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/atlas-3.10.1/build/..//include -I/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/atlas-3.10.1/build/..//include/contrib -DAdd_ -DF77_INTEGER=int -DStringSunStyle -DATL_OS_OSX -DATL_ARCH_Corei2 -DATL_CPUMHZ=2300 -DATL_AVX -DATL_SSE3 -DATL_SSE2 -DATL_SSE1 -DATL_USE64BITS -DATL_GAS_x8664 -DATL_DYLIBS -DPentiumCPS=2300 -DATL_FULL_LAPACK -DATL_NCPU=4 -O3 -fomit-frame-pointer -fPIC -fvectorize -fslp-vectorize -march=native -mavx  -o xgmmsearch gmmsearch.o
./xgmmsearch -p s -r -1

[cooljeanius (Eric Gallager)]

Cc Me!

[McBeath@…]

Crash after r105312 was used

[McBeath@…]

Thanks for the patch. The first compile issue was fixed, but the regression fought back. There seems to be a -vectorize-loops which kills the build at a later stage. Please find attached the main.log

clang/llvm seems to be really broken

[Veence (Vincent)]

Indeed, and there is not much left to do, except banning the use of clang until these bigs are fixed…

Sigh…

[McBeath@…]

Cc Me!

[aranoya@…]

Thanks for the patch. As commented above, it now fails at a later stage. Main.log is attached.

Thanks

[aranoya@…]

crash after new port file

[aranoya@…]

Cc Me!

[Veence (Vincent)]

r105342 should disable clang as a possible compiler and reverts default choice to gcc47 for all machines. Please test and tell me.

[Veence (Vincent)]

PS: I really encourage you to report the clang bugs you found upstream. It is the only way to eventually get a version that will work and support AVX kernels (performace x2 w/r SSE).

[dhuffkc@…]

Replying to vince@…:

r105342 should disable clang as a possible compiler and reverts default choice to gcc47 for all machines. Please test and tell me.

Works for me...thanks!

--Don

[Veence (Vincent)]

Thanks. I’m going to commit a final patch and rev-bump the Portfile. I close this bug series. If anyone still experiences a problem, please reopen it.

r105428

[aranoya@…]

Replying to vince@…:

Thanks. I’m going to commit a final patch and rev-bump the Portfile. I close this bug series. If anyone still experiences a problem, please reopen it.

r105428

Thanks a lot, it worked for me as well.

[Veence (Vincent)]

Following r105491 that upgrades clang-3.3, I have re-enabled the +clang33 variant, but I have not bumped the revision yet. Please update, test and report any error you might find, especially on AVX (Core i2 +) machines.

Thanks !

[atif.azad@…]

Replying to vince@…:

This is a clear bug in clang/llvm-3.3. Try again with the new Portfile (r105312). If you still get the same error, you should report it to the clang/llvm developers.

I am also getting this error despite having the new file reported in that (r105312)

[atif.azad@…]

I have made the changes as per ​https://trac.macports.org/changeset/105342

However when I do "sudo port upgrade installed", I still get the same error message :

Selected C compiler: /opt/local/bin/gcc-mp-4.7 Selected F77 compiler: gfortran47 ---> Building atlas Error: org.macports.build for port atlas returned: command execution failed Please see the log file for port atlas for details:

/opt/local/var/macports/logs/_opt_local_var_macports_sources_svn.macports.org_trunk_dports_math_atlas/atlas/main.log

Error: Unable to upgrade port: 1

[mf2k (Frank Schima)]

Replying to atif.azad@…:

I have made the changes as per ​https://trac.macports.org/changeset/105342

What do you mean? Hopefully you simply ran.

sudo port selfupdate

However when I do "sudo port upgrade installed",

You should normally not upgrade all installed ports. You probably want to then run:

sudo port upgrade outdated

[mf2k (Frank Schima)]

Please don't re-open a fixed ticket without attaching a main.log.

Also, please use WikiFormatting in your comments.

[Veence (Vincent)]

Replying to atif.azad@…:

I have made the changes as per ​https://trac.macports.org/changeset/105342

However when I do "sudo port upgrade installed", I still get the same error message :

Selected C compiler: /opt/local/bin/gcc-mp-4.7 Selected F77 compiler: gfortran47

This ticket was about Atlas and Clang. It appears you use gcc47 to compile Atlas, so your issue is unrelated to this ticket. Please file a new bug and attach the log file if your problem persist.

[atif.azad@…]

Main.log

[atif.azad@…]

Please note that I am behind a proxy so had to run:

sudo port -d sync and now ran

sudo port upgrade outdated

Above I have attached the Main.log

[larryv (Lawrence Velázquez)]

You didn’t clean atlas, so this main.log is not useful. Please run sudo port clean atlas, open a new ticket, and attach the log there. This ticket does not apply to you.

[larryv (Lawrence Velázquez)]

Replying to vince@…:

This ticket was about Atlas and Clang. It appears you use gcc47 to compile Atlas, so your issue is unrelated to this ticket. Please file a new bug and attach the log file if your problem persist.

The new ticket is #39065, I think.

[cecilyen@…]

Cc Me!