I am trying to integrate a Matlab program I wrote into some Fortran code. I tried to follow the example Mathworks provides. But I can't get it to compile because I can't find the header files it requests.
Does anyone know of an example of someone getting it to work on Linux using an Intel compiler. I think that might be part of the problem because Matlab only supports GNU Fortran on Linux.
And I realize this is a simple question, I just don't understand how to do anything in compiling more complicated than including multiple files with defined paths.
Disclaimer: I'm currently using OS X so I can only provide output from OS X but everything should transfer easily over to Linux due to the Unix base. I also don't have the Intel Fortran compiler on OS X (only the C/C++ compiler).
Note: You will need to substitute the paths I use for the correct paths on your system depending on your MATLAB installation directory.
This issue isn't specific to the Intel Compiler, I also receive errors with the GCC Fortran compiler.
$ gfortran fengdemo.F
fengdemo.F:1:0:
#include "fintrf.h"
^
Fatal Error: fintrf.h: No such file or directory
compilation terminated.
You can use the Unix locate command to find files.
$ locate fintrf.h
/Applications/Matlab R2014a.app/extern/include/fintrf.h
In the directory where fengdemo.F is we can then pass the correct directory in using the -I option
-I../../include/
However, this produces linking errors as we haven't specified where the libraries for fintrf.h can be found. We can do this with the -L option (you will need to replace maci64 with the correct option for Linux - I can't remember it off the top of my head but you should be able to see it in the bin directory)
-L../../../bin/maci64/
Now we need to tell it what libraries to use with -leng -lmx and so the completed command is
$ ifort fengdemo.F -I../../include/ -L../../../bin/maci64/ -leng -lmx
and it should compile correctly.
We aren't finished yet though as it won't execute. We need to set up our PATH and DYLD_LIBRARY_PATH environment variables correctly. Specifically we need to add the bin and bin/maci64 directories of our MATLAB installation to PATH
$ export PATH=$PATH:/Applications/Matlab\ R2014a.app/bin/maci64:/Applications/Matlab\ R2014a.app/bin
and the bin/maci64/ and sys/os/maci64/ to DYLD_LIBRARY_PATH
$ export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:/Applications/Matlab\ R2014a.app/bin/maci64/:/Applications/Matlab\ R2014a.app/sys/os/maci64/
Note: On Linux DYLD_LIBRARY_PATH should be LD_LIBRARY_PATH. Thanks to Vladimir F for correcting me.
Now you can execute the program using
$ ./a.out
Related
i am new to stackflow and i previously i have no background in computer system and programming. However, now i need to run analysis under cygwin for my bioinformatics project. I encounter some error when i try to compile a file name 'zone_b.linux'using cygwin, to produce an executable program. The linux file is download from web https://github.com/haddocking/HADDOCK-binding-sites-tutorial/blob/master/ana_scripts/zone_b.linux. When i try to compile using the following command under cygwin it produce the following error:
$ gcc zone_b.linux
/usr/lib/gcc/i686-pc-cygwin/6.4.0/../../../libcygwin.a(libcmain.o): In
function `main':
/usr/src/debug/cygwin-2.9.0-3/winsup/cygwin/lib/libcmain.c:37: undefined
reference to `WinMain#16'
collect2: error: ld returned 1 exit status
Error description
I search the following error under stackoverflow, and i found two post with similar problem.
First is the post from undefined reference to `WinMain#16'. It stated that the problem is due the Microsoft'linker uses a runtime library entry point(winMainCRTStartup) that calls Microsoft's non-standard WinMain instead of standard main. So, i try the post's suggestion of including the entry by following command
$ gcc zone_b.linux /entry:winMainCRTStartup
gcc: error: /entry:winMainCRTStartup: No such file or directory
However i get the error no such file or directory. I think maybe it is because i am running under cygwin not mingW.
Second post is the Undefined reference to WinMain in Cygwin. From the post, it said use -c compile flag to only produce object file. However, for my case, i am not using any -c. Therefore, i think it is not relevant to my issue.
I would appreciate if anyone could kindly explain to me since i am new to this computing area. Thank you.
zone_b.linux is the compiled and linked executable program to run on a linux machine. It is a 32-bit ELF binary file. It will not work on a Windows machine, even using cygwin or mingw32, without re-compulation.
You probably have to compile zone_b.f, a FORTRAN source file, using the gfortran compiler to create a zone_b.exe that is usable in cygwin. I saw no instructions for this, but try something like gcc zone_b.f and cross fingers. Be sure gfortran is installed using cygwin setup.
You will also need to (re-)build the other executables (cluster_struc and contact) by performing make in the ana_scripts directory. Any supplied executables (from the git clone ... or a downloaded .zip file) will not work under cygwin.
You will need to have perl and python installed. I think perl is installed by default. You can install python2 using cygwin setup. The python script looked like it will work with python2 or python3, whichever is the default. On cygwin, today, python2 is the default python. I don't do perl, so cross your fingers.
I believe my question is similar to this post: Linux: cannot find lgfortran though gfortran is installed.
However, since the suggested answer does not fix my problem, there seems no other choice other than asking it again, for a desperate Linux new comer like me.
Here is the problem. I installed GNU fortran compiler 4.8.4 and can find it in terminal
$ which gfortran-4.8
/usr/bin/gfortran-4.8
and
$ locate gfortran
/usr/bin/gfortran-4.7
/usr/bin/gfortran-4.8
/usr/bin/x86_64-linux-gnu-gfortran-4.7
/usr/bin/x86_64-linux-gnu-gfortran-4.8
/usr/lib/gcc/x86_64-linux-gnu/4.7/libgfortran.a
/usr/lib/gcc/x86_64-linux-gnu/4.7/libgfortran.so
/usr/lib/gcc/x86_64-linux-gnu/4.7/libgfortran.spec
/usr/lib/gcc/x86_64-linux-gnu/4.7/libgfortranbegin.a
/usr/lib/gcc/x86_64-linux-gnu/4.8/libgfortran.a
/usr/lib/gcc/x86_64-linux-gnu/4.8/libgfortran.so
/usr/lib/gcc/x86_64-linux-gnu/4.8/libgfortran.spec
/usr/lib/gcc/x86_64-linux-gnu/4.8/libgfortranbegin.a
/usr/lib/x86_64-linux-gnu/libgfortran.so.3
/usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
/usr/share/doc/gfortran-4.7
/usr/share/doc/gfortran-4.8
/usr/share/doc/libgfortran-4.7-dev
/usr/share/doc/libgfortran-4.8-dev
/usr/share/doc/libgfortran3
/usr/share/man/man1/gfortran-4.7.1.gz
/usr/share/man/man1/gfortran-4.8.1.gz
/usr/share/man/man1/x86_64-linux-gnu-gfortran-4.7.1.gz
/usr/share/man/man1/x86_64-linux-gnu-gfortran-4.8.1.gz
/var/cache/apt/archives/gfortran-4.7_4.7.3-12ubuntu1_amd64.deb
/var/cache/apt/archives/gfortran-4.8_4.8.4-2ubuntu1~14.04_amd64.deb
/var/cache/apt/archives/libgfortran-4.7-dev_4.7.3-12ubuntu1_amd64.deb
/var/cache/apt/archives/libgfortran-4.8-dev_4.8.4-2ubuntu1~14.04_amd64.deb
/var/cache/apt/archives/libgfortran3_4.8.4-2ubuntu1~14.04_amd64.deb
/var/lib/dpkg/info/gfortran-4.7.list
/var/lib/dpkg/info/gfortran-4.7.md5sums
/var/lib/dpkg/info/gfortran-4.8.list
/var/lib/dpkg/info/gfortran-4.8.md5sums
/var/lib/dpkg/info/libgfortran-4.7-dev:amd64.list
/var/lib/dpkg/info/libgfortran-4.7-dev:amd64.md5sums
/var/lib/dpkg/info/libgfortran-4.8-dev:amd64.list
/var/lib/dpkg/info/libgfortran-4.8-dev:amd64.md5sums
/var/lib/dpkg/info/libgfortran3:amd64.list
/var/lib/dpkg/info/libgfortran3:amd64.md5sums
/var/lib/dpkg/info/libgfortran3:amd64.postinst
/var/lib/dpkg/info/libgfortran3:amd64.postrm
/var/lib/dpkg/info/libgfortran3:amd64.shlibs
/var/lib/dpkg/info/libgfortran3:amd64.symbols
So gfortran seems installed, although I don't understand why 4.7 version is still there after my removing it.
In setting Global Compiler Settings of Code:Blocks, when I choose GNU Fortran Compiler, and its Toolchain Executables, I tried the installation directory as
/usr
/usr/bin
and
/usr/lib/gcc/x86_64-linux-gnu/4.8/
as suggested in the previous post, Code:Blocks tell me
could not auto-detect installation path of "GNU Fortran Compiler".....
More details of compiler configuration is here in the image (Thanks to Mike's suggestion).
And here's the full list of compilers on my computer:
List of Compliers
Your posting shows that you have both gfortran-4.7 and gfortran-4.8
installed under /usr/bin.
Having multiple GCC Fortran compilers (or multiple C or C++ compilers) is
perfectly valid and commonplace. Code::Blocks will allow you configure
as many Fortran compilers as you have got, provided you give them different
names. It's also fine if you just want to configure one of them as the
"GNU Fortran Compiler" and ignore the others.
But in any case, Code::Blocks must be able to unambiguously identify the
installed compiler that you are calling "GNU Fortran Compiler". You
have specified the Compiler's installation directory as /usr/bin
and have left the Program files compiler name as gfortran.
There is no such compiler as /usr/bin/gfortran in your system,
and there is no program called gfortran anywhere in your PATH. You
have /usr/bin/gfortran-4.7 and /usr/bin/gfortran-4.8. As you have
installed both of them, Code::Blocks assumes you want both of them. It
can't tell which one of them you want to configure as "GNU Fortran Compiler".
So:-
Set Compiler's installation directory = /usr/bin
In Program files, change all occurrences of gfortran to gfortran-4.8,
if you want "GNU Fortran Compiler" to mean gfortran-4.8.
OK out.
Default compiler name in 20.3 version was mingw32-gfortran. However, the executable name coming with installation is x86_64-w64-mingw32-gfortran. If this is written in compiler settings. It works.enter image description here
The install file codeblocks-20.03mingw-setup installs the file gfortran.exe into the C:\Program Files\CodeBlocks\MinGW\bin directory. However the Settings>Compiler>toolchainexecutables autodetect function looks for mingw32-gfortran.exe.
To fix this, in toolchainexecutables, change the filename mingw32-gfortran.exe to gfortran.exe in 3 places, then autodetect will find it.
I'm currently trying to start learning ocaml with cygwin, but when I try to compile an ml file, nothing happens - no error messages and no files created.
The command I used on cygwin was,
$ ocamlc hello.ml
According to my Prof., there should be a file called, a.out created on my working folder, but there was nothing.
But when I tried with this command,
$ ocamlc -o a.out hello.ml
a.out file was created properly, and I could run the compiled program using
$ ./a.out
as pointed out by the Prof.
For some experiment, I typed in the following,
$ ocamlc -o a hello.ml
This created a file named 'a' without any file extension.
So my question is,
1. Why doesn't it create the a.out file in the first place? - it should have been done according to the Prof.
2. What does the .out file do?
Any new file created when you type ocamlc hello.ml? Maybe camlprog.exe around? If it is, you are using MinGW OCaml over Cygwin. MinGW OCaml is a windows app therefore its default executable file name is not a.out, which is the default name for Unix and Cygwin.
I never recommend ppl to learn OCaml with Windows or Cygwin. Since there are 3 flavors: Cygwin OCaml, MinGW OCaml and MSVC OCaml and they behave slightly different like this. And newcomers are never sure which flavor they are actually using.
Hi team,
I have three files which I need to compile for testing, btw im using CentOS linux.
source_code.c
library.h
library.c
how do I put the library.h in the gcc library, so I can use it?
how do I compile the source_code.c to use that library?
Thank you very much.
This is basic knowledge of your tools, but you can do this:
#include "library.h" in the include section of the library.c code (at top of the file).
gcc source_code.c library.c in the linux terminal will link and compile both source_code.c and library.c. This will generate an executable named "a.out" (if there were no compilation problems). You can change its name, by adding the option -o name to the gcc command (gcc source_code.c library.c -o mycode will generate an executable named "mycode").
If you really need a library that will be used by a lot of other programs, you can look for "shared libraries", but I think that you are asking for a basic thing.
You dont need this library.h while building and executable (with gcc) as you should have specified the exact location of the library in the source file. All you need to do is gcc sourcefile1.c sourcefile2.c -o exename
I am trying to compile a simple hello world program in Haskell, with Haskell Platform 2011.2.0.1. If I load the code in WinGHCi, and use the GUI to compile, the .exe is created. Then I can run the .exe from Cygwin.
But if I try to compile the code in Cygwin (using ghc --make), linker fails. But again, if I compile from the Windows cmd prompt, then the compile+linker works fine.
Are there any other environment variables I need to import into Cygwin, to make the compile+linker work in it? I have put the following dirs in my Cygwin PATH: 2011.2.0.1/lib/extralibs/bin, 2011.2.0.1/bin (these are the only two valid Haskell related entries that I could see in the Windows environment variables).
I also noticed a couple of invalid items in the Windows environment variables (this looks like a bug in the Haskell installation):
(system var) C/ProgramFiles/Haskell/bin - this dir does not exist because I have installed Haskell in D disk.
(user var) userxxx/ApplicationData/cabal/bin - this dir does not exist.
I tried to file a bug report in HaskellPlatform, but I dont have permission to do it.
Without access to your development environment or a listing of the errors that you're getting, I can only assume that the issue is related to the way that you've set up your PATH.
GHC on Windows comes bundled with its own gcc compiler (for C code) and ld linker. If you've installed Cygwin, you've probably also installed the MinGW toolchain, which comes with its own version of gcc and ld. Then, you've probably made your PATH variable list /usr/bin before the path to the Haskell Platform binary directories, which makes ghc find the MinGW linker and C compiler before it finds the versions that were bundled with GHC.
You need to make sure that the HP directories are listed before the Cygwin directories. It should not be like this:
$ echo $PATH
/bin:/usr/bin:.../2011.2.0.1/bin
Instead, it should be like this:
$ echo $PATH
.../2011.2.0.1/bin:/bin:/usr/bin
This is only a guess at what the issue might be, and you should provide more details for a better diagnosis.