I am trying to run the Woden Physics Example inside Pharo which involves getting Bullet properly compiled and the smalltalk bindings properly installed in Pharo.
I am using Linux Mint 17 x64.
But NativeBoost seems unable to load the compiled libraries. I have been using the sources provided here:
https://github.com/ronsaldo/bullet-pharo
https://github.com/ronsaldo/swig
I built the modified version of swig as well as the bullet libraries and bindings with the provided build scripts.
I also have doublechecked that the bullet libraries are 32 bit.
Opening up the Woden physics example returns this error:
failed to get a symbol address:
PharoNB_new_BTDefaultCollisionConfiguration__SWIG_1
When examining the call stack in the debugger, it turns out that the module handle is 0.
I verified this by executing the same message as
BulletCInterface nbLibraryNameOrHandle
executes:
NativeBoost forCurrentPlatform loadModule: 'BulletPharo'
This message returns 0. I tried to specify the full path to libPharoBullet.so in the workspace, like:
NativeBoost forCurrentPlatform loadModule:
'/home/martin/.local/share/Pharo/bullet-pharo/libBulletPharo.so'
with the same result. I also verified it with a 32 bit system library of mine (liblzma) and there NativeBoost was able to load it, as it returned a non-zero handle.
So i suspect something during compilation went wrong...
I also did
readelf -h libPharoBullet.so
and its ABI was "UNIX - GNU" while the ABI of pharo-vm is "UNIX - System V"
Could this be the problem here ?
How can i force the ABI to be System V when compiling ? I use gcc 4.8.2
Or what steps could i otherwise perform ?
Related
I have installed Google's or-tools on my Mac running 11.1 (Big Sur). When I run make test_cc, I get a long list with different results and also some messenges like ---- Integer programming example with CPLEX ---- Supports for solver CPLEX not linked in.
However, if I try an example from https://developers.google.com/optimization/introduction/cpp, I get the above error (see header) when trying to make and run the program (I have copy pasted the complete program). I have executed the make command with
Death-Star:or-tools me$ make run SOURCE=../Routing/Routing/main.cpp. ls ../Routing/Routing/main.cpp shows the file.
What have I done wrong?
or-tools version is 8.1.8487
I have an OCaml program that worked fine on Ubuntu 16 but when recompiled and run on Ubuntu 20 I get the following error:-
$ ocamldebug ./linearizer
OCaml Debugger version 4.08.1
(ocd) r
Loading program... done.
Time: 89534
Program end.
Uncaught exception: Sys_error "Illegal seek"
(ocd) b
Time: 89533 - pc: 624888 - module Netaccel_link
No source file for Netaccel_link.
I thought this was due to missing dev libraries but:-
$ sudo apt install libocamlnet-ocaml-dev
Reading package lists... Done
Building dependency tree
Reading state information... Done
libocamlnet-ocaml-dev is already the newest version (4.1.6-1build6).
0 upgraded, 0 newly installed, 0 to remove and 20 not upgraded.
What setup step am I missing on Ubuntu 20?
This looks like a regression bug in libocamlnet and you should report an issue there or, I am a bit pessimistic that you will get any response, you can try to debug the issue yourself.
The problem that you are facing has nothing to do with missing libraries (they will be reported during installation or, if the package is broken, end up in linker errors). It may result, however, from some misconfiguration of the system. If that is true, then you're lucky as you can fix it yourself.
I will give you some advice that might help you in debugging this issue. For more, please try using discuss.ocaml.org as a more suitable media (SO doesn't favor this kind of a discussion and we might get deleted by admins).
The illegal seek exception is thrown when the seek operation is applied on a non-regular file, aka ESPIPE Unix error. So check your inputs. It could be that what was previously regarded as a file in Ubuntu is now a pipe or a socket.
Try to use ltrace or strace to pinpoint the culprit e.g.,
ltrace ./linearizer
or, if it overwhelms you, try strace
strace ./linearizer
Instead of using ocamldebug you can use plain gdb. You can use gdb's interfaces to provide the path to the source code (though most likely it won't work since ocamlnet is not compiled with debug information). I believe that it will give you a more meaningful backtrace.
Instead of using the system installation try using opam. Install your dependencies with opam and try older versions as well as newer versions of the OCaml compiler. Also, try different versions of ocamlnet. Ideally, try to reproduce the environment that used to work for you.
When nothing else works, you can use objdump -d and look at the disassembly of your binary. OCaml is using a pretty readable and intuitive name mangling scheme (<module_name>__<function_name>_<uid>), so you can easily find the source code (search for <module_name>.ml file and look for the <function_name> there)
Finally, just use docker or any other container to run your application. Consider switching from ocamlnet to something more modern and supported.
I am currently installing the HDF5 library, more precisely the hdf5-1.10.0-patch1, on Cygwin, as I want to use it with Fortran. Following the instructions from the hdfgroup website
(here is the link), I did the following:
./configure --enable-fortran
make > "out1_check.txt" 2> "warn1_check.txt" &
make check > "out2_check.txt" 2> "warn2_check.txt" &
The execution of the last command (make check) proceeds as it should, until it gets stuck. The process does not stop and something is happening (8-12% CPU are in use by sh.exe, already 39 hours of CPU time) but "out2_check.txt" looks like
Making check in src
...
[many successful checks]
...
============================
No need to test testlinks_env.sh again.
============================
============================
Testing testswmr.sh
Unfortunately, I do not have the output file from the first run of make check, but it did not contain more information on Testing testswmr.sh. There was never any error message.
So, what is this testswmr.sh, why does it get stuck and how can I finalize the installation process? Maybe I can skip the remaining checks and just proceed to make install?
Important note: an older version of HDF5 is already installed from the Cygwin repo. It does not seem to support Fortran however, so I decided to install the current version myself.
Available (and used) compilers are gcc and gfortran.
As far as I can tell, only Intel Fortran is supported on Windows. There is no Cygwin download here https://support.hdfgroup.org/HDF5/release/obtain518.html and I have never come across a report of experience for Cygwin/Fortran/HDF5.
Your options:
Use Intel Fortran
Use Linux or Mac
Sorry
I start saying that i am a newbie in programming and then i am not sure i will be able to explain well my problem.
I had some c++ code i wrote, this code are loaded and used by some R functions.
To compile the code i used the following:
R CMD SHLIB MyCode.cpp
and i loaded the library in R with
dyn.load("MyCOde.so")
Sometimes i built also an R package and i was able to load it into R.
If i do all these stuff on a Mac with mountain lion everything work fine, but now that i switched to mavericks, i have some problems. The R CMD SHLIB MyCode.cpp command works but when i used dyn.load("MyCOde.so") i get the following text:
Errore in dyn.load(paste(dir_function, "MyCOde.so", sep = "")) :
unable to load shared object 'MyCOde.so':
dlopen(MyCOde.so, 6): Symbol not found: __ZNSt8ios_base4InitC1Ev
Referenced from: MyCOde.so
Expected in: flat namespace
in MyCOde.so
Moreover if i try to load the package in R, i get the following
ld: warning: directory not found for option '-L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2'
ld: library not found for -lquadmath
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [MyCode.so] Error 1
Can someone helps me?
Based on the helpful website of:
thecoatlessprofessor
Type this into your terminal shell:
curl -O http://r.research.att.com/libs/gfortran-4.8.2-darwin13.tar.bz2
sudo tar fvxz gfortran-4.8.2-darwin13.tar.bz2 -C /
This will create what you need to resume compiling as before.
Since it starts to work I can publish the answer for such a cases.
When you change the compiler and standard libraries - please note that different libraries have different implementation and different standard support. Changing the basement of your system might require total rebuild of your system with the new C++ standard library.
Your libraries are not the exception. So if have the errors in your linker like this:
warning: directory not found for option
'-L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2'
apply next algorithm:
Check whether the directory /usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 still exists. I bet it is not.
Check if you still have the libstdc++ from the missed compiler? Usually if you upgrade the same compiler and the C++ standard library ABI does not change everything should continue to work. If the ABI changed or you switch standard C++ library and compiler - you face the massive system rebuild.
Recompile your library and apps with the new C++ standard library and compiler.
I am using armadillo4.300.0. I am operating on a dense matrix of size 2840260x103. I am loading this matrix from a .csv file of size approximately 3.7GB. I have enabled "ARMA_64BIT_WORD" in my application as well as config.hpp under armadillo_bits directory.
#if !defined(ARMA_64BIT_WORD)
#define ARMA_64BIT_WORD
#endif
I am compiling with gcc49 and running on ubuntu 12.04. When I run I am getting the following error. Interestingly, the application occasionally runs too. For eg., if I keep trying for some 10 times, it runs sometime.
error: Mat::init(): requested size is too large
terminate called after throwing an instance of 'std::logic_error'
what(): Mat::init(): requested size is too large
Do I need to take care of something else?
Ramki.
This problem is solved with the Intel MKL library, when we compile with the -DMKL_ILP64 -m64. Typically we focus only on link flags. But it is important to note that these flags must be enabled during compile phase on the gcc command as well. I am not sure how to enable this on openmpi library. Also the lib armadillo.so must link with mkl_ilp64 instead of mkl_lp64. Follow the instruction below.
Building and installing armadillo :
export CXX=icpc
export CC=icpc
export PATH=$PATH:/home/ramki/intel/bin:
Edit $armadillo_root/cmake_aux/Modules/ARMA_FindMKL.cmake, include the PATHS correctly.
Edit $armadillo_root/cmake_aux/Modules/ARMA_FindMKL.cmake, change mkl_lp64 to mkl_ilp64
Edit $armadillo_root/CMakeLists.txt and (1) Change CMAKE_SHARED_LINKER_FLAGS to include the link line by intel link advisor and (2) Change CMAKE_CXX_FLAGS as given by intel link advisor
Run ./configure and make sure MKL library is used for blas and lapack, icpc to be the compiler and the rest to be alright.
Run make .
Verify the linked libraries by running ldd libarmadillo.so. Mainly verify whether it is linked with mkl_ilp64 library and mkl blas and lapack libraries.
Now run make install DESTDIR=local path.
This should work.