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JuliaOpt / CoinOptServices.jl

Julia interface to COIN-OR Optimization Services https://projects.coin-or.org/OS
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ERROR: CoinOptServices #25

Open zazadi opened 7 years ago

zazadi commented 7 years ago

Hi,

I am trying install CoinOptServices on a linux 64 bit system. But I get an error while building the package. The error is:

===========================[ ERROR: CoinOptServices ]===========================

LoadError: failed process: Process(patch -p1 -d .., ProcessExited(1)) [1] while loading /home/zazadi/.julia/v0.5/CoinOptServices/deps/build.jl, in expression starting on line 69

================================================================================

================================[ BUILD ERRORS ]================================

WARNING: CoinOptServices had build errors.

================================================================================

Thanks for your help! Zahra

tkelman commented 7 years ago

Sort of a duplicate of https://github.com/JuliaOpt/CoinOptServices.jl/issues/4. Try deleting /home/zazadi/.julia/v0.5/CoinOptServices/deps/src and /home/zazadi/.julia/v0.5/CoinOptServices/deps/usr then re-running Pkg.build("CoinOptServices").

zazadi commented 7 years ago 
===============================================[ ERROR: CoinOptServices ]================================================

LoadError: failed process: Process(`make`, ProcessExited(2)) [2]
while loading /home/zazadi/.julia/v0.5/CoinOptServices/deps/build.jl, in expression starting on line 69

=========================================================================================================================

====================================================[ BUILD ERRORS ]=====================================================

WARNING: CoinOptServices had build errors.

 - packages with build errors remain installed in /home/zazadi/.julia/v0.5
 - build the package(s) and all dependencies with `Pkg.build("CoinOptServices")`
 - build a single package by running its `deps/build.jl` script

===========================================================================================

I got this error after applying what you suggested.

tkelman commented 7 years ago

that's not the useful part of the error message. post the entire output to https://gist.github.com and leave a link here

zazadi commented 7 years ago

Here is the link: https://gist.github.com/zazadi/980cc024fd34dd6f0cc45fa365159aa9

Thanks,

On Wed, Nov 2, 2016 at 7:55 PM, Tony Kelman notifications@github.com wrote:

that's not the useful part of the error message. post the entire output to https://gist.github.com https://urldefense.proofpoint.com/v2/url?u=https-3A__gist.github.com&d=CwMCaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=2kf2-euD79hYvD-HezRW4OYGC3qwHXl9GPPfYCjQ1TI&m=pNpQmDPU1LUvddDlKSgmSIQF3S8jLsxbDoL2o6huBiI&s=LizAIIhpj_T1MthAazfW7gn77urZst4GYUVk6ve2btU&e= and leave a link here

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_JuliaOpt_CoinOptServices.jl_issues_25-23issuecomment-2D258034828&d=CwMCaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=2kf2-euD79hYvD-HezRW4OYGC3qwHXl9GPPfYCjQ1TI&m=pNpQmDPU1LUvddDlKSgmSIQF3S8jLsxbDoL2o6huBiI&s=NKu8fENI1wMSbSkkSTYMNfLQAqO6v1a1K9YI6euSLvQ&e=, or mute the thread https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AWH-5FeJZv0Cl-5Fz-2D4dPphVm76xASON12UAks5q6SL0gaJpZM4KmiqB&d=CwMCaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=2kf2-euD79hYvD-HezRW4OYGC3qwHXl9GPPfYCjQ1TI&m=pNpQmDPU1LUvddDlKSgmSIQF3S8jLsxbDoL2o6huBiI&s=X1fHyDr3J9F5vrsxF1RikzL9X3OjjPbkX3ryYEsB3YE&e= .

tkelman commented 7 years ago

make[2]: *** [FixPointConstructors.lo] Killed

that suggests you're running out of memory. What operating system and compiler version are you using?

zazadi commented 7 years ago

This is basically a high-performance computing cluster:

On Thu, Nov 3, 2016 at 9:00 AM, Tony Kelman notifications@github.com wrote:

make[2]: *\ [FixPointConstructors.lo] Killed

that suggests you're running out of memory. What operating system and compiler version are you using?

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_JuliaOpt_CoinOptServices.jl_issues_25-23issuecomment-2D258135498&d=CwMCaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=2kf2-euD79hYvD-HezRW4OYGC3qwHXl9GPPfYCjQ1TI&m=tp_wW8d319do2_Hjmre_nzx7syDm7045nqyxkppmRN4&s=ksQ0UavPJTNnJ-wRFJXKs9OukREuTlU4E_fIK8oGbTU&e=, or mute the thread https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AWH-5FeDfFt7hssw-2Ds9ZPK6mrJACHGhVYVks5q6drpgaJpZM4KmiqB&d=CwMCaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=2kf2-euD79hYvD-HezRW4OYGC3qwHXl9GPPfYCjQ1TI&m=tp_wW8d319do2_Hjmre_nzx7syDm7045nqyxkppmRN4&s=TXtyiaVw3sCzcSneCmPUKjceprRVosk4ck3yJbcaukc&e= .

zazadi commented 7 years ago

Also I checked my account available memory and I have about 95.8 GB.

On Thu, Nov 3, 2016 at 9:10 AM, Zahra Azadi zazadi@g.clemson.edu wrote:

This is basically a high-performance computing cluster:

  • Currently comprises 1,978 compute nodes (20,728 cores) + 598 NVIDIA Tesla GPU accelerators
  • InfiniBand and Myrinet network interconnects between compute nodes
  • Operating system on all nodes: Scientific Linux 6 (based on RedHat Enterprise Linux)

On Thu, Nov 3, 2016 at 9:00 AM, Tony Kelman notifications@github.com wrote:

make[2]: *\ [FixPointConstructors.lo] Killed

that suggests you're running out of memory. What operating system and compiler version are you using?

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_JuliaOpt_CoinOptServices.jl_issues_25-23issuecomment-2D258135498&d=CwMCaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=2kf2-euD79hYvD-HezRW4OYGC3qwHXl9GPPfYCjQ1TI&m=tp_wW8d319do2_Hjmre_nzx7syDm7045nqyxkppmRN4&s=ksQ0UavPJTNnJ-wRFJXKs9OukREuTlU4E_fIK8oGbTU&e=, or mute the thread https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AWH-5FeDfFt7hssw-2Ds9ZPK6mrJACHGhVYVks5q6drpgaJpZM4KmiqB&d=CwMCaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=2kf2-euD79hYvD-HezRW4OYGC3qwHXl9GPPfYCjQ1TI&m=tp_wW8d319do2_Hjmre_nzx7syDm7045nqyxkppmRN4&s=TXtyiaVw3sCzcSneCmPUKjceprRVosk4ck3yJbcaukc&e= .

tkelman commented 7 years ago

Do you have a low memory ulimit or something? It's getting killed while compiling the C++ library, which suggests you wouldn't be able to build couenne outside of Julia either.

zazadi commented 7 years ago

But I have about 98.5 GB free memory!

On Thu, Nov 3, 2016 at 9:12 AM, Tony Kelman notifications@github.com wrote:

Do you have a low memory ulimit or something? It's getting killed while compiling the C++ library, which suggests you wouldn't be able to build couenne outside of Julia either.

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_JuliaOpt_CoinOptServices.jl_issues_25-23issuecomment-2D258138061&d=CwMCaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=2kf2-euD79hYvD-HezRW4OYGC3qwHXl9GPPfYCjQ1TI&m=6CQJOHRIhRS7CZqFYnAtIYoiDvGG0IhEoqanIY4wdsw&s=vjNSsOh0DdoAuTXtM_atvrBX78AqfSfb3yhIZ4-9OoA&e=, or mute the thread https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AWH-5FeOjqDeo85IcQWhvWW50bwgBMuy56ks5q6d3EgaJpZM4KmiqB&d=CwMCaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=2kf2-euD79hYvD-HezRW4OYGC3qwHXl9GPPfYCjQ1TI&m=6CQJOHRIhRS7CZqFYnAtIYoiDvGG0IhEoqanIY4wdsw&s=fFXyY3n_i3XoJ0us-JzmewvGfZ18ktjB6exCfZbQx7I&e= .

tkelman commented 7 years ago

If the ulimit is set really low then processes might get killed anyway. Sysadmins on giant clusters seem to love setting low ulimits, I guess so one person can't use all of the memory? If you are able to read dmesg you'll probably see the out-of-memory or ulimit killer terminating the compiler here.

Maybe you could try submitting a small compute job to do the compilation, since the ulimits are probably specific to the login nodes.

zazadi commented 7 years ago

I see that before installing Julia I should have some required dependencies such as GCC. Do you think that it might be the reason that I may miss some of them.

Thanks,

On Thu, Nov 3, 2016 at 9:24 AM, Tony Kelman notifications@github.com wrote:

If the ulimit is set really low then processes might get killed anyway. Sysadmins on giant clusters seem to love setting low ulimits, I guess so one person can't use all of the memory? If you are able to read dmesg you'll probably see the out-of-memory or ulimit killer terminating the compiler here.

Maybe you could try submitting a small compute job to do the compilation, since the ulimits are probably specific to the login nodes.

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_JuliaOpt_CoinOptServices.jl_issues_25-23issuecomment-2D258140706&d=CwMFaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=2kf2-euD79hYvD-HezRW4OYGC3qwHXl9GPPfYCjQ1TI&m=NG3H2xbuClYW-n8VikoB7_x2jkDlBJcGPuukYnqNN3c&s=qRHaBcMqP5NQb3s-jUZf7xoDQAz4WgHGpPSM5sdYx8A&e=, or mute the thread https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AWH-5FeMsNnZQ4QcYRuPO6YVHoAv4WKLguks5q6eB0gaJpZM4KmiqB&d=CwMFaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=2kf2-euD79hYvD-HezRW4OYGC3qwHXl9GPPfYCjQ1TI&m=NG3H2xbuClYW-n8VikoB7_x2jkDlBJcGPuukYnqNN3c&s=eo3XHWLzRfUucuzOpyWmtH4UJ_PXGhxoPEuAZR7CpIU&e= .

tkelman commented 7 years ago

No, that wouldn't successfully compile up to one particular C++ source file in the middle of Couenne and be killed there. Some user resource limit set too low by a sysadmin on your login node is killing the compiler process.

mattheu94 commented 7 years ago

Hi, i have a problema like this, my error message is that:

checking for COIN-OR package CoinDepend... skipped check via pkg-config, redirect to fallback checking for COIN-OR package CoinDepend (fallback)... no, dependency coinutils not available configure: error: Required package CoinUtils or Osi not available. configure: error: /bin/bash '../../SYMPHONY/configure' failed for SYMPHONY ===========================[ ERROR: CoinOptServices ]===========================

LoadError: failed process: Process(setenv(../configure --prefix=/home/cacciola/.julia/v0.5/CoinOptServices/deps/usr --enable-dependency-linking coin_skip_warn_cflags=yes coin_skip_warn_cxxflags=yes coin_skip_warn_fflags=yes '--with-coinutils-lib=-L/home/cacciola/.julia/v0.5/Cbc/deps/usr/lib -lCoinUtils' --with-coinutils-incdir=/home/cacciola/.julia/v0.5/Cbc/deps/usr/lib/../include/coin '--with-osi-lib=-L/home/cacciola/.julia/v0.5/Cbc/deps/usr/lib -lOsi -lCoinUtils' --with-osi-incdir=/home/cacciola/.julia/v0.5/Cbc/deps/usr/lib/../include/coin '--with-clp-lib=-L/home/cacciola/.julia/v0.5/Cbc/deps/usr/lib -lClp -lOsiClp' --with-clp-incdir=/home/cacciola/.julia/v0.5/Cbc/deps/usr/lib/../include/coin '--with-cgl-lib=-L/home/cacciola/.julia/v0.5/Cbc/deps/usr/lib -lCgl' --with-cgl-incdir=/home/cacciola/.julia/v0.5/Cbc/deps/usr/lib/../include/coin '--with-cbc-lib=-L/home/cacciola/.julia/v0.5/Cbc/deps/usr/lib -lCbc' --with-cbc-incdir=/home/cacciola/.julia/v0.5/Cbc/deps/usr/lib/../include/coin '--with-blas=-L/home/cacciola/.julia/v0.5/Ipopt/deps/usr/lib -lcoinblas' '--with-lapack=-L/home/cacciola/.julia/v0.5/Ipopt/deps/usr/lib -lcoinlapack' '--with-mumps-lib=-L/home/cacciola/.julia/v0.5/Ipopt/deps/usr/lib -lcoinmumps' '--with-ipopt-lib=-L/home/cacciola/.julia/v0.5/Ipopt/deps/usr/lib -lipopt',String["PATH=/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games","PWD=/home/cacciola","SHELL=/bin/sh","SSH_CONNECTION=93.32.74.180 62035 10.0.0.8 22","OPENBLAS_NUM_THREADS=8","MAIL=/var/mail/cacciola","LANG=it_IT.UTF-8","LOGNAME=cacciola","XDG_RUNTIME_DIR=/run/user/1006","XDG_SESSION_ID=706","PKG_CONFIG_PATH=/home/cacciola/.julia/v0.5/Cbc/deps/usr/lib/pkgconfig:/home/cacciola/.julia/v0.5/Ipopt/deps/usr/lib/pkgconfig","SSH_CLIENT=93.32.74.180 62035 22","USER=cacciola","SSH_TTY=/dev/pts/2","HOME=/home/cacciola","TERM=xterm","OPENBLAS_MAIN_FREE=1"]), ProcessExited(1)) [1] while loading /home/cacciola/.julia/v0.5/CoinOptServices/deps/build.jl, in expression starting on line 69

================================================================================

================================[ BUILD ERRORS ]================================

WARNING: CoinOptServices had build errors.

================================================================================

rickyars commented 7 years ago

@mattheu94 did you find a solution? i have the same problem.

tkelman commented 7 years ago

installing pkg-config might help

rickyars commented 7 years ago

@tkelman it is installed - that's the weird thing

tkelman commented 7 years ago

gist the entire build log and config.log files