Im struggling with Jupyter Kernel dying after executing a cell with Random Forest and MAE, MAPE, RMSE codes on a VirtualMachine (with 11gb RAM deslocated for it).
The strange part is that two cells of my code have instances of Random Forest. I wasnt getting this error in the first instance, only in the second Random Forest cell. After updating some packages (numpy, scikit-learn, jupyter... ) trying to solve I cant even execute the first Random Forest cell anymore.
The message I get is "kernel appears to have died and will restart automatically" and no other tips about which package is causing the issue.
I even deleted the entire virtualenv and create a new one with conda, and still having the error.
Anyone have a clue in what to do or some alternative so I can progress with the project?
Thanks!
Related
I'm new to Anylogic and created a simple traffic model. Only use 'carSource', 'CarMoveTo', 'Car Dispose' blocks to set the car routes. But After I ran the model, it worked for a while, then all the cars froze without any error occurring. ’Events‘ panel also stopped. How to solve it?
Most likely your model is running into an infinite loop somewhere in the logic. The first place to check would be all your loops that might become infinite,e.g Do loops, Do-while loops, iterator for loops where you perhaps change the counter variable manually...
If you have the professional version of AnyLogic the best option is to run the model in debug mode until you get this to the point where it freezes and then press pause. You will then see where in the code the model is getting stuck.
If this does not work you might need to start putting traceln in major functions and see ing you can spot the last traceln that gets printed and keep on adding more and more until you can find the point between two traceln where the model freezes
I had the same problem, that after a certain time, all cars froze and there wasn't a signle error.
The problem on my side was that the stop line was too close to the intersection, so I moved it a little bit farther.
My DES model was working well till I've added a new function (just like many others added before) and the model gave me all these error messages:
I wonder what do these messages mean and what made all of them appear suddenly. I was running the model just before it without any errors. Is there a way I could get my model back? :)
Thank you.
Edit 1:
Here is the newly created function: Newly created function
Given that I've ignored it, and made all the callings of it as comments, then the errors were still appearing. I've closed this model version and opened a backup then created the same function and the whole scenario happened again with the same 94 errors.
Is there something I need to change in the function itself?
The function checks the number of agents in certain parts of the model to stop delay blocks accordingly. That's done by adding variables that increment on exiting of agents and get the difference between them.
Typically this is caused by a syntax error in the new function that you created. See if you ignore this and then compile if it gets fixed.
Most of the time the compiler is smart enough to show you the error, but often if you replace a { with [ or you leave out a { the compiler get very confused and gives you 100s of errors.
If yous still cant find the issue maybe paste the code of your new function in the question.
Since a couple of days, I constantly receive the same error while using MATLAB which happens at some point with dlopen. I am pretty new to MATLAB, and that is why I don't know what to do. Google doesn't seem to be helping me either. When I try to make an eigenvector, I get this:
Error using eig
LAPACK loading error:
dlopen: cannot load any more object with static TLS
I also get this while making a multiplication:
Error using *
BLAS loading error:
dlopen: cannot load any more object with static TLS
I did of course look for the solutions to this problem, but I don't understand too much and don't know what to do. These are threads I found:
How do I use the BLAS library provided by MATLAB?
http://www.mathworks.de/de/help/matlab/matlab_external/calling-lapack-and-blas-functions-from-mex-files.html
Can someone help me please?
Examples of function calls demonstrating this error
>> randn(3,3)
ans =
2.7694 0.7254 -0.2050
-1.3499 -0.0631 -0.1241
3.0349 0.7147 1.4897
>> eig(ans)
Error using eig
LAPACK loading error:
dlopen: cannot load any more object with static TLS
That's bug no 961964 of MATLAB known since R2012b (8.0). MATLAB dynamically loads some libs with static TLS (thread local storage, e.g. see gcc compiler flag -ftls-model). Loading too many such libs => no space left.
Until now mathwork's only workaround is to load the important(!) libs first by using them early (they suggest to put "ones(10)*ones(10);" in startup.m). I better don't comment on this "solution strategy".
Since R2013b (8.2.0.701) with Linux x86_64 my experience is: Don't use "doc" (the graphical help system)! I think this doc-utility (libxul, etc.) is using a lot of static TLS memory.
Here is an update (2013/12/31)
All the following tests were done with Fedora 20 (with glibc-2.18-11.fc20) and Matlab 8.3.0.73043 (R2014a Prerelease).
For more information on TLS, see
Ulrich Drepper, ELF handling For Thread-Local Storage, Version 0.21, 2013,
currently available at Akkadia and Redhat.
What happens exactly?
MATLAB dynamically (with dlopen) loads several libraries that need tls initialization. All those libs need a slot in the dtv (dynamic thread vector). Because MATLAB loads several of these libs dynamically at runtime at compile/link time the linker (at mathworks) had no chance to count the slots needed (that's the important part). Now it's the task of the dynamic lib loader to handle such a case at runtime. But this is not easy. To cite dl-open.c:
For static TLS we have to allocate the memory here and
now. This includes allocating memory in the DTV. But we
cannot change any DTV other than our own. So, if we
cannot guarantee that there is room in the DTV we don't
even try it and fail the load.
There is a compile time constant (called DTV_SURPLUS, see glibc-source/sysdeps/generic/ldsodefs.h) in the glibc's dynamic lib loader for reserving a number of additional slots for such a mess (dynamically loading libs with static TLS in a multithreading program). In the glibc-Version of Fedora 20 this value is 14.
Here are the first libs (running MATLAB) that needed dtv slots in my case:
matlabroot/bin/glnxa64/libut.so
/lib64/libstdc++.so.6
/lib64/libpthread.so.0
matlabroot/bin/glnxa64/libunwind.so.8
/lib64/libuuid.so.1
matlabroot/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so
matlabroot/sys/java/jre/glnxa64/jre/lib/amd64/libfontmanager.so
matlabroot/sys/java/jre/glnxa64/jre/lib/amd64/libt2k.so
matlabroot/bin/glnxa64/mkl.so
matlabroot/sys/os/glnxa64/libiomp5.so
/lib64/libasound.so.2
matlabroot/sys/jxbrowser/glnxa64/xulrunner/xulrunner-linux-64/libxul.so
/lib64/libselinux.so.1
/lib64/libpixman-1.so.0
/lib64/libEGL.so.1
/lib64/libGL.so.1
/lib64/libglapi.so.0
Yes more than 14 => too many => no slot left in the dtv. That's what the error message tries to tell us and especially mathworks.
For the record: In order not to violate MATLAB's license I didn't debug, decompile or disassemble any part of the binaries shipped with MATLAB. I only debugged the free and open glibc-binaries of Fedora 20 that MATLAB were using to dynamically load the libs.
What can be done, to solve this problem?
There are 3 options:
(a)
Rebuild MATLAB and do not dynamically load those libs
(with initial-exec tls model) instead link against them (then the linker
can count the required slots!)
(b)
Rebuild those libs and ensure they are NOT using the initial-exec tls model.
(c)
Rebuild glibc and increase DTV_SURPLUS in
glibc/sysdeps/generic/ldsodefs.h
Obviously options (a) and (b) can only be done by mathworks.
For option (c) no source of MATLAB is needed and thus can be done without mathworks.
What is the status at mathworks?
I really tried to explain this to the "MathWorks Technical Support Department". But my impression is: they don't understand me. They closed my support ticket and suggested a telephone(!) conversation in January 2014 with a technical support manager.
I'll do my very best to explain this, but to be honest: I'm not very confident.
Update (2014/01/10): Currently mathworks is trying option (b).
Update (2014/03/19): For the file libiomp5.so you can download a newly compiled version (without static TLS) at mathworks, bug report 961964. And the other libs? No improvement there. So don't be suprised to get "dlopen: cannot load any more object with static TLS" with "doc", e.g. see bug report 1003952.
Restarting Matlab solved the problem for me.
long story short: in the directory that you start matlab from create a file
startup.m with content ones(10)*ones(10);. Restart matlab and it will be taken care of.
This is, as I find, an age-old problem yet unsolved by MathWorks.
Here are my two cents, which worked for me (when I wanted IT++ external libraries, with MEX).
Let the library that you found to be the cause of the problem be "libXYZ.so", and that you know where it lies on your system.
The solution is to inform MATLAB to load the specific library at the earliest of its startup. The reason for this error is apparently due to the lack of slots for this thread local storage aka tls purpose (due to they already been filled-up).
Because the latest compilations suddenly required a new library that was not loaded earlier during its startup, MATLAB throws up this error.
Pity that MATLAB never cared to resolve this problem so long.
Fortunately, the solution is a single, very simple terminal command.
Typical steps on a linux-machine should be as follows:
Open command prompt (Ctrl+Alt+T in Ubuntu)
Issue the following command
export LD_PRELOAD=<PATH-TO-libxyz.so>
e.g.: export LD_PRELOAD=/usr/local/lib/libitpp.so
Start matlab from the same terminal
matlab &
Running your program now should resolve the issue, as it is for my case.
Good luck!
Reference:
[1] http://au.mathworks.com/matlabcentral/answers/125117-openmp-mex-files-static-tls-problem
http://www.mathworks.de/support/bugreports/961964 has been updated on 30/01/2014.
There is a zip file attached with libiomp5.so
I tested it on Mageia 4 x86_64 with Matlab R2013b.
I can now use the Documentation of Matlab to open a demo without any problem.
I had the same problem and I think I just solved it.
When installing matlab use the custom installation (I did not do this the first time). Choose to create symbolic links to matlab scripts in the predefined folder (/usr/local/bin). This did the trick for me!
I had the same problem with both Matlab 2013b and Matlab 2014a. The fix provided by mathworks for libiomp5.so only removed the problem of LAPACK not working. However, I could not use external libraries which are using OpenMp (such as VL_FEAT): I still get the error
"dlopen: cannot load any more object with static TLS."
The only thing which worked for me was downgrading to Matlab 2012b.
I came across this problem after "bar" (for bar plots) with a an array gives me just a single blue block, with no errors thrown. Reboot at first solved the problem. But after a memory error (after processing a very large file), I just cannot get past this blue block problem.
Using "hist" on a matrix input gives me the "BLAS loading error" problem and led me to this thread. The Mathwork workaround fixed the hist and bar problems.
Just wanted to bring recognition to the extent of this bug's influence.
I had the same problem and solved it by increasing my Java Heap memory. Go to Preferences > General > Java-Heap Memory, and increase the allocated memory.
Increasing Java heap memory (to 512 mb) also worked for me on R2013b/Ubuntu 12.04. The "BLAS loading error" began when I processed an 11 GB file (with 16 GB RAM), and has not recurred after increasing java heap memory and restarting matlab.
Since a couple of days, I constantly receive the same error while using MATLAB which happens at some point with dlopen. I am pretty new to MATLAB, and that is why I don't know what to do. Google doesn't seem to be helping me either. When I try to make an eigenvector, I get this:
Error using eig
LAPACK loading error:
dlopen: cannot load any more object with static TLS
I also get this while making a multiplication:
Error using *
BLAS loading error:
dlopen: cannot load any more object with static TLS
I did of course look for the solutions to this problem, but I don't understand too much and don't know what to do. These are threads I found:
How do I use the BLAS library provided by MATLAB?
http://www.mathworks.de/de/help/matlab/matlab_external/calling-lapack-and-blas-functions-from-mex-files.html
Can someone help me please?
Examples of function calls demonstrating this error
>> randn(3,3)
ans =
2.7694 0.7254 -0.2050
-1.3499 -0.0631 -0.1241
3.0349 0.7147 1.4897
>> eig(ans)
Error using eig
LAPACK loading error:
dlopen: cannot load any more object with static TLS
That's bug no 961964 of MATLAB known since R2012b (8.0). MATLAB dynamically loads some libs with static TLS (thread local storage, e.g. see gcc compiler flag -ftls-model). Loading too many such libs => no space left.
Until now mathwork's only workaround is to load the important(!) libs first by using them early (they suggest to put "ones(10)*ones(10);" in startup.m). I better don't comment on this "solution strategy".
Since R2013b (8.2.0.701) with Linux x86_64 my experience is: Don't use "doc" (the graphical help system)! I think this doc-utility (libxul, etc.) is using a lot of static TLS memory.
Here is an update (2013/12/31)
All the following tests were done with Fedora 20 (with glibc-2.18-11.fc20) and Matlab 8.3.0.73043 (R2014a Prerelease).
For more information on TLS, see
Ulrich Drepper, ELF handling For Thread-Local Storage, Version 0.21, 2013,
currently available at Akkadia and Redhat.
What happens exactly?
MATLAB dynamically (with dlopen) loads several libraries that need tls initialization. All those libs need a slot in the dtv (dynamic thread vector). Because MATLAB loads several of these libs dynamically at runtime at compile/link time the linker (at mathworks) had no chance to count the slots needed (that's the important part). Now it's the task of the dynamic lib loader to handle such a case at runtime. But this is not easy. To cite dl-open.c:
For static TLS we have to allocate the memory here and
now. This includes allocating memory in the DTV. But we
cannot change any DTV other than our own. So, if we
cannot guarantee that there is room in the DTV we don't
even try it and fail the load.
There is a compile time constant (called DTV_SURPLUS, see glibc-source/sysdeps/generic/ldsodefs.h) in the glibc's dynamic lib loader for reserving a number of additional slots for such a mess (dynamically loading libs with static TLS in a multithreading program). In the glibc-Version of Fedora 20 this value is 14.
Here are the first libs (running MATLAB) that needed dtv slots in my case:
matlabroot/bin/glnxa64/libut.so
/lib64/libstdc++.so.6
/lib64/libpthread.so.0
matlabroot/bin/glnxa64/libunwind.so.8
/lib64/libuuid.so.1
matlabroot/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so
matlabroot/sys/java/jre/glnxa64/jre/lib/amd64/libfontmanager.so
matlabroot/sys/java/jre/glnxa64/jre/lib/amd64/libt2k.so
matlabroot/bin/glnxa64/mkl.so
matlabroot/sys/os/glnxa64/libiomp5.so
/lib64/libasound.so.2
matlabroot/sys/jxbrowser/glnxa64/xulrunner/xulrunner-linux-64/libxul.so
/lib64/libselinux.so.1
/lib64/libpixman-1.so.0
/lib64/libEGL.so.1
/lib64/libGL.so.1
/lib64/libglapi.so.0
Yes more than 14 => too many => no slot left in the dtv. That's what the error message tries to tell us and especially mathworks.
For the record: In order not to violate MATLAB's license I didn't debug, decompile or disassemble any part of the binaries shipped with MATLAB. I only debugged the free and open glibc-binaries of Fedora 20 that MATLAB were using to dynamically load the libs.
What can be done, to solve this problem?
There are 3 options:
(a)
Rebuild MATLAB and do not dynamically load those libs
(with initial-exec tls model) instead link against them (then the linker
can count the required slots!)
(b)
Rebuild those libs and ensure they are NOT using the initial-exec tls model.
(c)
Rebuild glibc and increase DTV_SURPLUS in
glibc/sysdeps/generic/ldsodefs.h
Obviously options (a) and (b) can only be done by mathworks.
For option (c) no source of MATLAB is needed and thus can be done without mathworks.
What is the status at mathworks?
I really tried to explain this to the "MathWorks Technical Support Department". But my impression is: they don't understand me. They closed my support ticket and suggested a telephone(!) conversation in January 2014 with a technical support manager.
I'll do my very best to explain this, but to be honest: I'm not very confident.
Update (2014/01/10): Currently mathworks is trying option (b).
Update (2014/03/19): For the file libiomp5.so you can download a newly compiled version (without static TLS) at mathworks, bug report 961964. And the other libs? No improvement there. So don't be suprised to get "dlopen: cannot load any more object with static TLS" with "doc", e.g. see bug report 1003952.
Restarting Matlab solved the problem for me.
long story short: in the directory that you start matlab from create a file
startup.m with content ones(10)*ones(10);. Restart matlab and it will be taken care of.
This is, as I find, an age-old problem yet unsolved by MathWorks.
Here are my two cents, which worked for me (when I wanted IT++ external libraries, with MEX).
Let the library that you found to be the cause of the problem be "libXYZ.so", and that you know where it lies on your system.
The solution is to inform MATLAB to load the specific library at the earliest of its startup. The reason for this error is apparently due to the lack of slots for this thread local storage aka tls purpose (due to they already been filled-up).
Because the latest compilations suddenly required a new library that was not loaded earlier during its startup, MATLAB throws up this error.
Pity that MATLAB never cared to resolve this problem so long.
Fortunately, the solution is a single, very simple terminal command.
Typical steps on a linux-machine should be as follows:
Open command prompt (Ctrl+Alt+T in Ubuntu)
Issue the following command
export LD_PRELOAD=<PATH-TO-libxyz.so>
e.g.: export LD_PRELOAD=/usr/local/lib/libitpp.so
Start matlab from the same terminal
matlab &
Running your program now should resolve the issue, as it is for my case.
Good luck!
Reference:
[1] http://au.mathworks.com/matlabcentral/answers/125117-openmp-mex-files-static-tls-problem
http://www.mathworks.de/support/bugreports/961964 has been updated on 30/01/2014.
There is a zip file attached with libiomp5.so
I tested it on Mageia 4 x86_64 with Matlab R2013b.
I can now use the Documentation of Matlab to open a demo without any problem.
I had the same problem and I think I just solved it.
When installing matlab use the custom installation (I did not do this the first time). Choose to create symbolic links to matlab scripts in the predefined folder (/usr/local/bin). This did the trick for me!
I had the same problem with both Matlab 2013b and Matlab 2014a. The fix provided by mathworks for libiomp5.so only removed the problem of LAPACK not working. However, I could not use external libraries which are using OpenMp (such as VL_FEAT): I still get the error
"dlopen: cannot load any more object with static TLS."
The only thing which worked for me was downgrading to Matlab 2012b.
I came across this problem after "bar" (for bar plots) with a an array gives me just a single blue block, with no errors thrown. Reboot at first solved the problem. But after a memory error (after processing a very large file), I just cannot get past this blue block problem.
Using "hist" on a matrix input gives me the "BLAS loading error" problem and led me to this thread. The Mathwork workaround fixed the hist and bar problems.
Just wanted to bring recognition to the extent of this bug's influence.
I had the same problem and solved it by increasing my Java Heap memory. Go to Preferences > General > Java-Heap Memory, and increase the allocated memory.
Increasing Java heap memory (to 512 mb) also worked for me on R2013b/Ubuntu 12.04. The "BLAS loading error" began when I processed an 11 GB file (with 16 GB RAM), and has not recurred after increasing java heap memory and restarting matlab.
I am controlling a pilot plant of boiler through Matlab using modbus RTU (serial communication).
I am running my control program (in editor) for 45 mins through a loop but I am facing two problems :
1] I can't change any variable value while running program which is deadly needed.
2] I am unable to see real time data in workspace while running script.
It updates all variables after finishing execution time. For my application I want data to appear for every iteration.
I couldn't solve them so I switched to simulink but that was even more frustrating.
In simulink I used user defined blocks (embedded Matlab function) to generate modbus address PDU which does not support to in-built matlab functions (like dec2hex).
Will please someone let me know in simulink, serial send/receive support which data format?(ASCII/HEX/DEC)
If you want to see the status of your system after each iteration this can be solved by putting a breakpoint there. If required you can even change the value of variables then.