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Published 20 hours ago • verified publisher icon scipopt

how to run JSCIP test exmple on macbook

Open usact opened this issue 4 years ago • 39 comments

Hi, I am trying to run JSCIP on MacBook.

My OS :

 MacOS Mojave  (10.14.6)

My java:

openjdk version "1.8.0_222" 
OpenJDK Runtime Environment (AdoptOpenJDK)(build 1.8.0_222-b10)
OpenJDK 64-Bit Server VM (AdoptOpenJDK)(build 25.222-b10, mixed mode)

I downloaded SCIP from

  https://scip.zib.de/download.php?fname=scipoptsuite-6.0.2.tgz

and build it after installing gmp. I just run :

  make

and then

  make test

It works well on MacBook.

Then, I installed JSCIP on macbook by following this step by step:

  https://github.com/SCIP-Interfaces/JSCIPOpt/blob/master/INSTALL.md

When I am running

java -cp scip.jar:examples.jar <"Linear" or "Quadratic" or "Read" or "Multiknapsack">

I got :

  -bash: syntax error near unexpected token `newline'

When I run

    java -cp scip.jar:examples.jar "Linear"

I got:

  A fatal error has been detected by the Java Runtime Environment:##  SIGSEGV (0xb) at pc=0x000000012138b319, pid=88434, tid=0x0000000000001d03

How can I run this correctly ?

Thanks

usact avatar Mar 11 '20 15:03 usact

Can you compile the SCIP Optimization Suite via

cd scipoptsuite-6.0.2
mkdir build; cd build
cmake ..
make

and try again? Could you also add the full log when compiling JSCIPOpt? Thanks!

mueldgog avatar Mar 11 '20 15:03 mueldgog

Hi, The log is to long, could you please let me know what parts are important ?

usact avatar Mar 11 '20 17:03 usact

Direct the output to a file and upload it here.

usact [email protected] schrieb am Mi., 11. März 2020, 18:59:

Hi, The log is to long, could you please let me know what parts are important ?

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mueldgog avatar Mar 11 '20 18:03 mueldgog

I have rebuilt JSCIPOpt.

I run:

  cmake .. -DSCIP_DIR=/Users/my_name/scipoptsuite-6.0.2/build > JSCIPOpt_cmake_log.txt

got:

  CMake Warning (dev):
  Policy CMP0042 is not set: MACOSX_RPATH is enabled by default.  Run "cmake
  --help-policy CMP0042" for policy details.  Use the cmake_policy command to
   set the policy and suppress this warning.

   MACOSX_RPATH is not specified for the following targets:

   jscip

   This warning is for project developers.  Use -Wno-dev to suppress it.

then, I run

    make > JSCIPOpt_make_log.txt

I got:

   ld: warning: directory not found for option '-L/Users/my_name/git/JSCIPOpt/lib'

I am not sure why I got this.

The log files are attached.

thanks JSCIPOpt_cmake_log.txt JSCIPOpt_make_log.txt

usact avatar Mar 11 '20 20:03 usact

Hi, I have posted it on github https://github.com/SCIP-Interfaces/JSCIPOpt/issues/21

thanks

On Wed, Mar 11, 2020 at 11:21 AM Benjamin Mueller [email protected] wrote:

Direct the output to a file and upload it here.

usact [email protected] schrieb am Mi., 11. März 2020, 18:59:

Hi, The log is to long, could you please let me know what parts are important ?

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usact avatar Mar 11 '20 21:03 usact

Did anybody find something wrong in the attached build log files ? thanks!

usact avatar Mar 12 '20 21:03 usact

I just tested it on our Mac machine, which uses

java -version
java version "1.8.0_131"
Java(TM) SE Runtime Environment (build 1.8.0_131-b11)
Java HotSpot(TM) 64-Bit Server VM (build 25.131-b11, mixed mode)

cmake -version
cmake version 3.13.3

gcc --version
Configured with: --prefix=/Library/Developer/CommandLineTools/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 10.0.0 (clang-1000.10.44.4)
Target: x86_64-apple-darwin17.7.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin

I get the same error message about "-L..." directory not found and the warning about MACOSX_RPATH, which don't seem relevant for the issue.

Anyway, executing

java -cp scip.jar:examples.jar "Linear"
feasible solution found by trivial heuristic after 0,0 seconds, objective value 2,000000e+00
presolving:
(round 1, fast)       1 del vars, 1 del conss, 0 add conss, 1 chg bounds, 0 chg sides, 0 chg coeffs, 0 upgd conss, 0 impls, 0 clqs
presolving (2 rounds: 2 fast, 1 medium, 1 exhaustive):
 2 deleted vars, 1 deleted constraints, 0 added constraints, 1 tightened bounds, 0 added holes, 0 changed sides, 0 changed coefficients
 0 implications, 0 cliques
presolved problem has 0 variables (0 bin, 0 int, 0 impl, 0 cont) and 0 constraints
transformed objective value is always integral (scale: 1)
Presolving Time: 0,00

 time | node  | left  |LP iter|LP it/n| mem |mdpt |frac |vars |cons |cols |rows |cuts |confs|strbr|  dualbound   | primalbound  |  gap   
t 0,0s|     1 |     0 |     0 |     - | 544k|   0 |   - |   0 |   0 |   0 |   0 |   0 |   0 |   0 |-1,000000e+01 |-1,000000e+01 |   0,00%

SCIP Status        : problem is solved [optimal solution found]
Solving Time (sec) : 0,00
Solving Nodes      : 1
Primal Bound       : -1,00000000000000e+01 (2 solutions)
Dual Bound         : -1,00000000000000e+01
Gap                : 0,00 %
final gap = 0.0
solution (x,y) = (2.0, 4.0) with objective value -10.0
solution (x,y) = (2.0, 0.0) with objective value 2.0

works just fine. I'm not too familiar with Mac and Java, so I cannot help you too much with the issue.

mueldgog avatar Mar 13 '20 08:03 mueldgog

Can you add all the output of the java -cp scip.jar:examples.jar "Linear", please? I think that after A fatal error has been detected by the Java Runtime Environment: there is also an error log mention. Please add the file to the issue.

mueldgog avatar Mar 13 '20 08:03 mueldgog

Hi, 

I run the same command and got the error as follows. I have attached the log report.

thanks

java -cp scip.jar:examples.jar "Linear"

A fatal error has been detected by the Java Runtime Environment:

SIGSEGV (0xb) at pc=0x000000010d4bd319, pid=52939, tid=0x0000000000002703

JRE version: OpenJDK Runtime Environment (8.0_222-b10) (build 1.8.0_222-b10)

Java VM: OpenJDK 64-Bit Server VM (25.222-b10 mixed mode bsd-amd64 compressed oops)

Problematic frame:

C [libawt_lwawt.dylib+0x48319] JNI_OnLoad+0x91

Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again

An error report file with more information is saved as:

/Users/my_name/git/JSCIPOpt/build/Release/hs_err_pid52939.log

If you would like to submit a bug report, please visit:

http://bugreport.java.com/bugreport/crash.jsp

The crash happened outside the Java Virtual Machine in native code.

See problematic frame for where to report the bug.

Abort trap: 6

gcc --version

 Configured with: --prefix=/Library/Developer/CommandLineTools/usr --with-gxx-include-dir=/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/c++/4.2.1

 Apple LLVM version 10.0.1 (clang-1001.0.46.4)

 Target: x86_64-apple-darwin18.7.0

 Thread model: posix

InstalledDir: /Library/Developer/CommandLineTools/usr/bin

cmake --version

  cmake version 3.16.5

  CMake suite maintained and supported by Kitware (kitware.com/cmake).

hs_err_pid52939.log

usact avatar Mar 13 '20 15:03 usact

Did you try ulimit -c unlimited ?

usact [email protected] schrieb am Fr., 13. März 2020, 16:03:

Hi, I run the same command and got :----------------------------java -cp scip.jar:examples.jar "Linear"## A fatal error has been detected by the Java Runtime Environment:## SIGSEGV (0xb) at pc=0x000000010d4bd319, pid=52939, tid=0x0000000000002703## JRE version: OpenJDK Runtime Environment (8.0_222-b10) (build 1.8.0_222-b10)# Java VM: OpenJDK 64-Bit Server VM (25.222-b10 mixed mode bsd-amd64 compressed oops)# Problematic frame:# C [libawt_lwawt.dylib+0x48319] JNI_OnLoad+0x91## Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again## An error report file with more information is saved as:# /Users/my_name/git/JSCIPOpt/build/Release/hs_err_pid52939.log## If you would like to submit a bug report, please visit:# http://bugreport.java.com/bugreport/crash.jsp# The crash happened outside the Java Virtual Machine in native code.# See problematic frame for where to report the bug.#Abort trap: 6---------------------------gcc --version Configured with: --prefix=/Library/Developer/CommandLineTools/usr --with-gxx-include-dir=/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/c++/4.2.1 Apple LLVM version 10.0.1 (clang-1001.0.46.4) Target: x86_64-apple-darwin18.7.0 Thread model: posix InstalledDir: /Library/Developer/CommandLineTools/usr/bincmake --version cmake version 3.16.5 CMake suite maintained and supported by Kitware ( kitware.com/cmake).

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mueldgog avatar Mar 13 '20 15:03 mueldgog

Hi,

I run the same command and got the error as follows. More details and the error log file can be found at https://github.com/SCIP-Interfaces/JSCIPOpt/issues/21

thanks,

java -cp scip.jar:examples.jar "Linear"

A fatal error has been detected by the Java Runtime Environment:

SIGSEGV (0xb) at pc=0x000000010d4bd319, pid=52939, tid=0x0000000000002703

JRE version: OpenJDK Runtime Environment (8.0_222-b10) (build

1.8.0_222-b10)

Java VM: OpenJDK 64-Bit Server VM (25.222-b10 mixed mode bsd-amd64

compressed oops)

Problematic frame:

C [libawt_lwawt.dylib+0x48319] JNI_OnLoad+0x91

Failed to write core dump. Core dumps have been disabled. To enable core

dumping, try "ulimit -c unlimited" before starting Java again

An error report file with more information is saved as:

/Users/my_name/git/JSCIPOpt/build/Release/hs_err_pid52939.log

If you would like to submit a bug report, please visit:

http://bugreport.java.com/bugreport/crash.jsp

The crash happened outside the Java Virtual Machine in native code.

See problematic frame for where to report the bug.

Abort trap: 6

gcc --version

 Configured with: --prefix=/Library/Developer/CommandLineTools/usr

--with-gxx-include-dir=/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/c++/4.2.1

 Apple LLVM version 10.0.1 (clang-1001.0.46.4)

 Target: x86_64-apple-darwin18.7.0

 Thread model: posix

InstalledDir: /Library/Developer/CommandLineTools/usr/bin

cmake --version

  cmake version 3.16.5

  CMake suite maintained and supported by Kitware (kitware.com/cmake).

On Fri, Mar 13, 2020 at 1:40 AM Benjamin Mueller [email protected] wrote:

Can you add all the output of the java -cp scip.jar:examples.jar "Linear", please? I think that after A fatal error has been detected by the Java Runtime Environment: there is also an error log mention. Please add the file to the issue.

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usact avatar Mar 13 '20 15:03 usact

yes,  java -cp scip.jar:examples.jar "Linear" ulimit -c unlimited

The error log file is attached. thanks,  Jinxu hs_err_pid54054.log

usact avatar Mar 13 '20 15:03 usact

yes,

java -cp scip.jar:examples.jar "Linear" ulimit -c unlimited

The error log file is attached. https://github.com/SCIP-Interfaces/JSCIPOpt/issues/21

thanks,

Jinxu

On Fri, Mar 13, 2020 at 8:07 AM Benjamin Mueller [email protected] wrote:

Did you try ulimit -c unlimited ?

usact [email protected] schrieb am Fr., 13. März 2020, 16:03:

Hi, I run the same command and got :----------------------------java -cp scip.jar:examples.jar "Linear"## A fatal error has been detected by the Java Runtime Environment:## SIGSEGV (0xb) at pc=0x000000010d4bd319, pid=52939, tid=0x0000000000002703## JRE version: OpenJDK Runtime Environment (8.0_222-b10) (build 1.8.0_222-b10)# Java VM: OpenJDK 64-Bit Server VM (25.222-b10 mixed mode bsd-amd64 compressed oops)# Problematic frame:# C [libawt_lwawt.dylib+0x48319] JNI_OnLoad+0x91## Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again## An error report file with more information is saved as:# /Users/my_name/git/JSCIPOpt/build/Release/hs_err_pid52939.log## If you would like to submit a bug report, please visit:# http://bugreport.java.com/bugreport/crash.jsp# The crash happened outside the Java Virtual Machine in native code.# See problematic frame for where to report the bug.#Abort trap: 6---------------------------gcc --version Configured with: --prefix=/Library/Developer/CommandLineTools/usr

--with-gxx-include-dir=/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/c++/4.2.1

Apple LLVM version 10.0.1 (clang-1001.0.46.4) Target: x86_64-apple-darwin18.7.0 Thread model: posix InstalledDir: /Library/Developer/CommandLineTools/usr/bincmake --version cmake version 3.16.5 CMake suite maintained and supported by Kitware ( kitware.com/cmake).

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usact avatar Mar 13 '20 15:03 usact

I don't see the log, where is it? Sorry, I might not see it because I use my phone.

It looks like that you added the ulimit ... to the java command. Just to be sure: You need to set the ulimit first and then execute the java command.

mueldgog avatar Mar 13 '20 15:03 mueldgog

i have run it:

$ulimit -c unlimited

and then $ java -cp scip.jar:examples.jar "Linear"

A fatal error has been detected by the Java Runtime Environment:

SIGSEGV (0xb) at pc=0x0000000123280319, pid=55309, tid=0x0000000000002203

JRE version: OpenJDK Runtime Environment (8.0_222-b10) (build 1.8.0_222-b10) Java VM: OpenJDK 64-Bit Server VM (25.222-b10 mixed mode bsd-amd64 compressed oops) Problematic frame: C [libawt_lwawt.dylib+0x48319] JNI_OnLoad+0x91

Core dump written. Default location: /cores/core or core.55309

An error report file with more information is saved as: /Users/my_name/git/JSCIPOpt/build/Release/hs_err_pid55309.log

If you would like to submit a bug report, please visit: http://bugreport.java.com/bugreport/crash.jsp The crash happened outside the Java Virtual Machine in native code. See problematic frame for where to report the bug.

Abort trap: 6 (core dumped)

usact avatar Mar 13 '20 15:03 usact

I have run it:

$ulimit -c unlimited

and then

$ java -cp scip.jar:examples.jar "Linear"

A fatal error has been detected by the Java Runtime Environment:

SIGSEGV (0xb) at pc=0x0000000123280319, pid=55309, tid=0x0000000000002203

JRE version: OpenJDK Runtime Environment (8.0_222-b10) (build 1.8.0_222-b10) Java VM: OpenJDK 64-Bit Server VM (25.222-b10 mixed mode bsd-amd64 compressed oops) Problematic frame: C [libawt_lwawt.dylib+0x48319] JNI_OnLoad+0x91

Core dump written. Default location: /cores/core or core.55309

An error report file with more information is saved as: /Users/my_name/git/JSCIPOpt/build/Release/hs_err_pid55309.log

If you would like to submit a bug report, please visit: http://bugreport.java.com/bugreport/crash.jsp The crash happened outside the Java Virtual Machine in native code. See problematic frame for where to report the bug.

Abort trap: 6 (core dumped)

On Fri, Mar 13, 2020 at 8:43 AM Benjamin Mueller [email protected] wrote:

I don't see the log, where is it? Sorry, I might not see it because I use my phone.

It looks like that you added the ulimit ... to the java command. Just to be sure: You need to set the ulimit first and then execute the java command.

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usact avatar Mar 13 '20 15:03 usact

What is written in /Users/my_name/git/JSCIPOpt/build/Release/hs_err_pid55309.log ?

usact [email protected] schrieb am Fr., 13. März 2020, 16:52:

i have run it:

$ulimit -c unlimited

$ java -cp scip.jar:examples.jar "Linear" A fatal error has been detected by the Java Runtime Environment: SIGSEGV (0xb) at pc=0x0000000123280319, pid=55309, tid=0x0000000000002203 JRE version: OpenJDK Runtime Environment (8.0_222-b10) (build 1.8.0_222-b10) Java VM: OpenJDK 64-Bit Server VM (25.222-b10 mixed mode bsd-amd64 compressed oops) Problematic frame: C [libawt_lwawt.dylib+0x48319] JNI_OnLoad+0x91 Core dump written. Default location: /cores/core or core.55309 An error report file with more information is saved as: /Users/my_name/git/JSCIPOpt/build/Release/hs_err_pid55309.log If you would like to submit a bug report, please visit: http://bugreport.java.com/bugreport/crash.jsp The crash happened outside the Java Virtual Machine in native code. See problematic frame for where to report the bug.

Abort trap: 6 (core dumped)

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mueldgog avatar Mar 13 '20 15:03 mueldgog

Okay, I have seen that you added the log to a previous post.

mueldgog avatar Mar 13 '20 15:03 mueldgog

Could it be that you have multiple versions of the java jdk installed? According to the error log, it looks like that there is some jenkins related jdk somewhere used. Could this be?

mueldgog avatar Mar 13 '20 16:03 mueldgog

You mean this ?

Internal exceptions (2 events):

200 Event: 0.039 Thread 0x00007fc223006800 Exception <a 'java/lang/NoSuchMethodError': Method sun.misc.Unsafe.defineClass(Ljava/lang /String;[BII)Ljava/lang/Class; name or signature does not match> (0x000000076ab07cb8) thrown at [/Users/jenkins/workspace/build- scripts/jobs/jdk8u/jdk8u-mac-x64-hotsp

201 Event: 0.039 Thread 0x00007fc223006800 Exception <a 'java/lang/NoSuchMethodError': Method sun.misc.Unsafe.prefetchRead(Ljava/lan g/Object;J)V name or signature does not match> (0x000000076ab07fa0) thrown at [/Users/jenkins/workspace/build-scripts/jobs/jdk8u /jdk8u-mac-x64-hotspot/workspace/build

usact avatar Mar 13 '20 16:03 usact

But, I do not have this folder: /Users/jenkins

on my laptop (macbook pro)

usact avatar Mar 13 '20 16:03 usact

You mean this ?

Internal exceptions (2 events):

200 Event: 0.039 Thread 0x00007fc223006800 Exception <a 'java/lang/NoSuchMethodError': Method sun.misc.Unsafe.defineClass(Ljava/lang /String;[BII)Ljava/lang/Class; name or signature does not match> (0x000000076ab07cb8) thrown at [/Users/jenkins/workspace/build- scripts/jobs/jdk8u/jdk8u-mac-x64-hotsp

201 Event: 0.039 Thread 0x00007fc223006800 Exception <a 'java/lang/NoSuchMethodError': Method sun.misc.Unsafe.prefetchRead(Ljava/lan g/Object;J)V name or signature does not match> (0x000000076ab07fa0) thrown at [/Users/jenkins/workspace/build-scripts/jobs/jdk8u /jdk8u-mac-x64-hotspot/workspace/build

But, I do not have this folder: /Users/jenkins

on my laptop (macbook pro)

On Fri, Mar 13, 2020 at 9:03 AM Benjamin Mueller [email protected] wrote:

Could it be that you have multiple versions of the java jdk installed? According to the error log, it looks like that there is some jenkins related jdk somewhere used. Could this be?

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usact avatar Mar 13 '20 16:03 usact

this is the latest error log file attached:

hs_err_pid55309.log

usact avatar Mar 13 '20 16:03 usact

this is the latest error log file attached.

On Fri, Mar 13, 2020 at 9:03 AM Benjamin Mueller [email protected] wrote:

Could it be that you have multiple versions of the java jdk installed? According to the error log, it looks like that there is some jenkins related jdk somewhere used. Could this be?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/SCIP-Interfaces/JSCIPOpt/issues/21#issuecomment-598796031, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALIY2AIC5LE7PEOUOVAPGQTRHJKMTANCNFSM4LFX4TSQ .

usact avatar Mar 13 '20 16:03 usact

I do not see that I have multiple JDKs ?

usact avatar Mar 13 '20 16:03 usact

The directory does not exist? Very strange. You should try to figure out why java wants to call something from there. Maybe you could reinstall the jdk? Check also your PATH and LD_LIBRARY_PATH variable (maybe there is something else for Mac).

usact [email protected] schrieb am Fr., 13. März 2020, 17:33:

this is the latest error log file attached.

On Fri, Mar 13, 2020 at 9:03 AM Benjamin Mueller <[email protected]

wrote:

Could it be that you have multiple versions of the java jdk installed? According to the error log, it looks like that there is some jenkins related jdk somewhere used. Could this be?

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mueldgog avatar Mar 13 '20 16:03 mueldgog

These are the values for the two env variables:

echo $PATH /Users/my_name/.pyenv/versions/3.5.4/lib/python3.5/site-packages/pyspark:/Users/my_name/.jenv/versions/1.8/bin:/Users/my_name/Work_2019_7_18/tools/scala/scala-2.12.3/bin:/usr/local/Cellar/pyenv-virtualenv/1.1.3/shims:/Users/my_name/.pyenv/shims:/Users/my_name/.jenv/shims:/Users/my_name/.jenv/bin:/Users/my_name/.jenv/shims:/Users/my_name/Work_2019_7_18/tools/maven/apache-maven-3.6.1/bin:/Users/my_name/.jenv/bin:~/.pyenv/versions/3.5.0/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin/scala/bin

$ echo $LD_LIBRARY_PATH

It is not set yet.

usact avatar Mar 13 '20 17:03 usact

Also, I have installed "docker desktop" on my laptop. Hope that it is not a problem.

usact avatar Mar 13 '20 17:03 usact

Also, I have tried to run a simple test Hello-World Java Program on my laptop. It works well.

usact avatar Mar 13 '20 17:03 usact

Would it be possible for you to create a new user account on your Mac that has no additional packages installed? I think that the current issue is due to some incompatibilities of some installed packages.

usact [email protected] schrieb am Fr., 13. März 2020, 18:17:

Also, I have tried to run a simple test Hello-World Java Program on my laptop. It works well.

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mueldgog avatar Mar 13 '20 17:03 mueldgog