[MacPorts] #38820: port atlas fails to upgrade
#38820: port atlas fails to upgrade -----------------------+-------------------------------- Reporter: aranoya@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Keywords: | Port: atlas -----------------------+-------------------------------- 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 -- Ticket URL: <https://trac.macports.org/ticket/38820> MacPorts <http://www.macports.org/> Ports system for OS X
#38820: port atlas fails to upgrade ------------------------+--------------------- Reporter: aranoya@… | Owner: vince@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Resolution: | Keywords: Port: atlas | ------------------------+--------------------- Changes (by macsforever2000@…): * owner: macports-tickets@… => vince@… * cc: aranoya@… (removed) Old description:
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
New description: 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 -- Comment: In the future, please use WikiFormatting. -- Ticket URL: <https://trac.macports.org/ticket/38820#comment:2> MacPorts <http://www.macports.org/> Ports system for OS X
#38820: port atlas fails to upgrade ------------------------+--------------------- Reporter: aranoya@… | Owner: vince@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Resolution: | Keywords: Port: atlas | ------------------------+--------------------- Comment (by 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. -- Ticket URL: <https://trac.macports.org/ticket/38820#comment:4> MacPorts <http://www.macports.org/> Ports system for OS X
#38820: port atlas fails to upgrade ------------------------+--------------------- Reporter: aranoya@… | Owner: vince@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Resolution: | Keywords: Port: atlas | ------------------------+--------------------- Comment (by vince@…): I’ve disabled the vectorizing flags for clang3.3 in r105324. Please retry (everyone). -- Ticket URL: <https://trac.macports.org/ticket/38820#comment:5> MacPorts <http://www.macports.org/> Ports system for OS X
#38820: port atlas fails to upgrade ------------------------+--------------------- Reporter: aranoya@… | Owner: vince@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Resolution: | Keywords: Port: atlas | ------------------------+--------------------- Comment (by vince@…): This is definitly 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 }}} -- Ticket URL: <https://trac.macports.org/ticket/38820#comment:6> MacPorts <http://www.macports.org/> Ports system for OS X
#38820: port atlas fails to upgrade ------------------------+--------------------- Reporter: aranoya@… | Owner: vince@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Resolution: | Keywords: Port: atlas | ------------------------+--------------------- Comment (by McBeath@…): Thanks for the patch. The first compile issue was fixed, but the regression fought back. Ther seems to be a -vectorize-loops which kills the build at a later state. Please find attached the main.log clang/llvm seems to be really broken -- Ticket URL: <https://trac.macports.org/ticket/38820#comment:8> MacPorts <http://www.macports.org/> Ports system for OS X
#38820: port atlas fails to upgrade ------------------------+--------------------- Reporter: aranoya@… | Owner: vince@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Resolution: | Keywords: Port: atlas | ------------------------+--------------------- Comment (by vince@…): Indeed, and there is not much left to do, except banning the use of clang until these bigs are fixed… Sigh… -- Ticket URL: <https://trac.macports.org/ticket/38820#comment:9> MacPorts <http://www.macports.org/> Ports system for OS X
#38820: port atlas fails to upgrade ------------------------+--------------------- Reporter: aranoya@… | Owner: vince@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Resolution: | Keywords: Port: atlas | ------------------------+--------------------- Comment (by aranoya@…): Thanks for the patch. As commented above, it now fails at a later stage. Main.log is attached. Thanks -- Ticket URL: <https://trac.macports.org/ticket/38820#comment:11> MacPorts <http://www.macports.org/> Ports system for OS X
#38820: port atlas fails to upgrade ------------------------+--------------------- Reporter: aranoya@… | Owner: vince@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Resolution: | Keywords: Port: atlas | ------------------------+--------------------- Comment (by vince@…): r105342 should disable clang as a possible compiler and reverts default choice to gcc47 for all machines. Please test and tell me. -- Ticket URL: <https://trac.macports.org/ticket/38820#comment:13> MacPorts <http://www.macports.org/> Ports system for OS X
#38820: port atlas fails to upgrade ------------------------+--------------------- Reporter: aranoya@… | Owner: vince@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Resolution: | Keywords: Port: atlas | ------------------------+--------------------- Comment (by vince@…): 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). -- Ticket URL: <https://trac.macports.org/ticket/38820#comment:14> MacPorts <http://www.macports.org/> Ports system for OS X
#38820: port atlas fails to upgrade ------------------------+--------------------- Reporter: aranoya@… | Owner: vince@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Resolution: | Keywords: Port: atlas | ------------------------+--------------------- Comment (by dhuffkc@…): Replying to [comment:13 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 -- Ticket URL: <https://trac.macports.org/ticket/38820#comment:15> MacPorts <http://www.macports.org/> Ports system for OS X
#38820: port atlas fails to upgrade ------------------------+--------------------- Reporter: aranoya@… | Owner: vince@… Type: defect | Status: closed Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Resolution: fixed | Keywords: Port: atlas | ------------------------+--------------------- Changes (by vince@…): * status: new => closed * resolution: => fixed Comment: 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 -- Ticket URL: <https://trac.macports.org/ticket/38820#comment:16> MacPorts <http://www.macports.org/> Ports system for OS X
#38820: port atlas fails to upgrade ------------------------+--------------------- Reporter: aranoya@… | Owner: vince@… Type: defect | Status: closed Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Resolution: fixed | Keywords: Port: atlas | ------------------------+--------------------- Comment (by aranoya@…): Replying to [comment:16 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. -- Ticket URL: <https://trac.macports.org/ticket/38820#comment:17> MacPorts <http://www.macports.org/> Ports system for OS X
#38820: port atlas fails to upgrade ------------------------+--------------------- Reporter: aranoya@… | Owner: vince@… Type: defect | Status: closed Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Resolution: fixed | Keywords: Port: atlas | ------------------------+--------------------- Comment (by vince@…): 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 ! -- Ticket URL: <https://trac.macports.org/ticket/38820#comment:18> MacPorts <http://www.macports.org/> Ports system for OS X
#38820: port atlas fails to upgrade ------------------------+--------------------- Reporter: aranoya@… | Owner: vince@… Type: defect | Status: closed Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Resolution: fixed | Keywords: Port: atlas | ------------------------+--------------------- Comment (by atif.azad@…): Replying to [comment:4 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) -- Ticket URL: <https://trac.macports.org/ticket/38820#comment:19> MacPorts <http://www.macports.org/> Ports system for OS X
#38820: port atlas fails to upgrade ------------------------+--------------------- Reporter: aranoya@… | Owner: vince@… Type: defect | Status: closed Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Resolution: fixed | Keywords: Port: atlas | ------------------------+--------------------- Comment (by 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 -- Ticket URL: <https://trac.macports.org/ticket/38820#comment:20> MacPorts <http://www.macports.org/> Ports system for OS X
#38820: port atlas fails to upgrade ------------------------+---------------------- Reporter: aranoya@… | Owner: vince@… Type: defect | Status: reopened Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Resolution: | Keywords: Port: atlas | ------------------------+---------------------- Changes (by atif.azad@…): * status: closed => reopened * resolution: fixed => -- Ticket URL: <https://trac.macports.org/ticket/38820#comment:21> MacPorts <http://www.macports.org/> Ports system for OS X
#38820: port atlas fails to upgrade ------------------------+---------------------- Reporter: aranoya@… | Owner: vince@… Type: defect | Status: reopened Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Resolution: | Keywords: Port: atlas | ------------------------+---------------------- Comment (by macsforever2000@…): Replying to [comment:20 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 }}} -- Ticket URL: <https://trac.macports.org/ticket/38820#comment:22> MacPorts <http://www.macports.org/> Ports system for OS X
#38820: port atlas fails to upgrade ------------------------+--------------------- Reporter: aranoya@… | Owner: vince@… Type: defect | Status: closed Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Resolution: fixed | Keywords: Port: atlas | ------------------------+--------------------- Changes (by macsforever2000@…): * status: reopened => closed * resolution: => fixed Comment: Please don't re-open a fixed ticket without attaching a main.log. Also, please use WikiFormatting in your comments. -- Ticket URL: <https://trac.macports.org/ticket/38820#comment:23> MacPorts <http://www.macports.org/> Ports system for OS X
#38820: port atlas fails to upgrade ------------------------+--------------------- Reporter: aranoya@… | Owner: vince@… Type: defect | Status: closed Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Resolution: fixed | Keywords: Port: atlas | ------------------------+--------------------- Comment (by vince@…): Replying to [comment:20 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. -- Ticket URL: <https://trac.macports.org/ticket/38820#comment:24> MacPorts <http://www.macports.org/> Ports system for OS X
#38820: port atlas fails to upgrade ------------------------+--------------------- Reporter: aranoya@… | Owner: vince@… Type: defect | Status: closed Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Resolution: fixed | Keywords: Port: atlas | ------------------------+--------------------- Comment (by 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 -- Ticket URL: <https://trac.macports.org/ticket/38820#comment:25> MacPorts <http://www.macports.org/> Ports system for OS X
#38820: port atlas fails to upgrade ------------------------+--------------------- Reporter: aranoya@… | Owner: vince@… Type: defect | Status: closed Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Resolution: fixed | Keywords: Port: atlas | ------------------------+--------------------- Comment (by larryv@…): 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. -- Ticket URL: <https://trac.macports.org/ticket/38820#comment:26> MacPorts <http://www.macports.org/> Ports system for OS X
#38820: port atlas fails to upgrade ------------------------+--------------------- Reporter: aranoya@… | Owner: vince@… Type: defect | Status: closed Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Resolution: fixed | Keywords: Port: atlas | ------------------------+--------------------- Comment (by larryv@…): Replying to [comment:24 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. -- Ticket URL: <https://trac.macports.org/ticket/38820#comment:27> MacPorts <http://www.macports.org/> Ports system for OS X
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