i want to use pthreads in my fortran program but i cannot even get it to compile. i have used pthreads in C programs and need it for my fortran program but a call to use f_pthread results in the following error:
Fatal Error: Can't open module file 'f_pthread.mod' for reading at (1): No such file or directory
so quite obviously i don't have f_pthread.mod linking. where is f_pthread.mod and/or how do i go about making it or downloading it? every single thing i have looked up talks about how to use pthreads in fortran, with a 'use f_pthread' at the beginning of the example program, but i cannot seem to figure out how they correctly link that module.
I've only ever come across the module f_pthread on IBM/AIX installations. If you have such an installation then the extensive IBM documentation should point you towards it. If you don't have, what makes you think you have that module ? Where does your compiler on your platform (you tell us neither) put module files ? Have you looked for f_pthread.mod there ?
Why do you 'need' pthreads for your Fortran program ? It would be much easier to use OpenMP, and there are only a few things that pthreads can do that OpenMP can't and which most Fortran programs are likely to want to do.
Related
I have a Fortran code which has been made to work on CPUs, but I need to accelerate it using GPUs and I chose to do that with OpenACC.
This code uses FFTW libraries when compiled with gfortran. However, as you may know, these libraries cannot be used with nvfortran. So, I have to go with cufft libraries.
Therefore, I used this conversion giude. The problem is, fftw allows users to build a Fortran module with iso_c_binding including the file fftw.f, while cufft does not have this kind of feature and you need to include the cufft.h header.
When compiling with nvfortran (I use -cpp, -Mfree, -lcufft and -l cufftw flags, checked the include and lib directories given to -I and -L flags) I get many errors:
The paths in all the #include inside the cufft.h file are wrong and I had to change them manually
All the comments ("//") in the header files are seen as errors (had to remove them manually)
“Label field of continuation line is not blank” errors everywhere in header files, starting from line 2 (in lines 1 I solved that giving 7 spaces - but didn’t I use -Mfree for that?)
Please help me, I don’t think that the right way to do so is to change files manually…
Thanks in advance for helping
You cannot include headers for the C programming language in Fortran source code. Instead use the Fortran interfaces to any libraries you need (provided such interfaces exist).
We ship a cuFFT interface module with the compilers. You should just be able to add "use cufft".
Full documentation can be found at: https://docs.nvidia.com/hpc-sdk/compilers/fortran-cuda-interfaces/index.html#cf-fft-runtime
Example codes are shipped with the NVHPC SDK which can be found in the "<INSTALL_DIR>/Linux_x86_64/<RELEASE>/examples/CUDA-Libraries/cuFFT/"" directory
I was having trouble with the linker for the embedded arm gcc compiler, and I found a tutorial somewhere online saying that I could fix my linker errors in arm-none-eabi-gcc by including the argument -specs=nosys.specs, which worked for me, and it was able to compile my code.
My chip is an ATSAM7SE256 microcontroller, which to my understanding is an arm7tdmi processor using the armv4t and thumb instruction sets, and I've been compiling my code using:
arm-none-eabi-gcc -march=armv4t -mtune=arm7tdmi -specs=nosys.specs -o <exe_name>.elf <input_files>
And the code compiles with no issue, but I have no idea if it's doing what I think it's doing.
What is the significance of a spec file? What other values can you set with -specs=, and in what situations would you want to? Is nosys.specs the value I want for a completely embedded arm microcontroller?
It is documented at: https://gcc.gnu.org/onlinedocs/gcc-11.1.0/gcc/Overall-Options.html#Overall-Options
It is a file containing switches to override standard defaults for various build components such as the compiler, assembler and linker. For example it can be used to replace the default C library.
I have never seen it used; typically bare-metal embedded system builds explicitly specify --nostdlib then explicitly link the required library. It could be used for environment specific build environments to link other default code such as an RTOS I guess. Personally I'd rather make all that explicit on the command line that hiding it in a file somewhere.
Essentially it applies the switches specified in the file as if they were defaults, so can be used to define defaults for specific build and execution environments.
The format of the specs file is documented at https://gcc.gnu.org/onlinedocs/gcc-11.1.0/gcc/Spec-Files.html#Spec-Files
Without seeing both the linker errors and the content of the nosys.specs file in this case it is difficult to say how or why it solved your linker problem. The alternative solution of course would be to apply whatever switches are in the specs file directly.
If you want to link a static library into an shared library or executable while keeping all the symbols visible (e.g. so you can dlopen it later to find them), a non-portable way to do this on Linux/BSD is to use the flag -Wl,--whole-archive. On macOS, the equivalent flag is -Wl,-force_load,<library>; on Windows it's apparently /WHOLEARCHIVE.
Is there a portable way to do this in CMake?
I know I can add linker flags with target_link_libraries. I can detect the OS. However, since the macOS version of this includes the library name in the same string as the flag (no spaces), I think this messes with CMake's usual handling of link targets and so on. The more compatible I try to make this, the more I have to bend over backwards to make it happen.
And this is without even getting into more unusual compilers like Intel, PGI, Cray, IBM, etc. Those may not be compilers that people commonly deal with, but in some domains it's basically unavoidable to need to deal with these.
Are there any better options?
flink.cmake will help you.
target_force_link_libraries(<target>
<PRIVATE|PUBLIC|INTERFACE> <item>...
[<PRIVATE|PUBLIC|INTERFACE> <item>...]...
)
I'm having trouble understanding if/how to share code among several Fortran projects without building libraries or duplicating source code.
I am using Eclipse/Photran with the Intel compiler (ifort) on a linux system, but I believe I'm having a bigger conceptual problem with modules than with the specific tools.
Here's a simple example: In ~/workspace/cow I have a source directory (src) containing cow.f90 (the PROGRAM) and two modules m_graze and m_moo in m_graze.f90 and m_moo.f90, respectively. This project builds and links properly to create the executable 'cow'. The executable and modules (m_graze.mod and m_moo.mod) are stored in ~/workspace/cow/Debug and object files are stored under ~/workspace/cow/Debug/src
Later, I create ~/workplace/sheep and have src/sheep.f90 as the program and src/m_baa.f90 as the module m_baa. I want to 'use m_graze, only: ruminate' in sheep.f90 to get access to the ruminate() subroutine. I could just copy m_graze.f90 but that could lead to code getting out of sync and doesn't take into account any dependencies m_graze might have. For these reasons, I'd rather leave m_graze in the cow project and compile and link sheep.f90 against it.
If I try to compile the sheep project, I'll get an error like:
error #7002: Error in opening the compiled module file. Check INCLUDE paths. [M_GRAZE]
Under Properties:Project References for sheep, I can select the cow project. Under Properties:Fortran Build:Settings:Intel Compiler:Preprocessor I can add ~/workspace/cow/Debug (location of the module files) to the list of include directories so the compiler now finds the cow modules and compiles sheep.f90. However the linker dies with something like:
Building target: sheep
Invoking: Intel(R) Fortran Linker
ifort -L/home/me/workspace/cow/Debug -o "sheep" ./src/sheep.o
./src/sheep.o: In function `sheep':
/home/me/workspace/sheep/src/sheep.f90:11: undefined reference to `m_graze_mp_ruminate_'
This would normally be solved by adding libraries and library paths to the linker settings except there are no appropriate libraries to link to (this is Fortran, not C.)
The cow project was perfectly capable of compiling and linking together cow.f90, m_graze.f90 and m_moo.f90 into an executable. Yet while the sheep project can compile sheep.f90 and m_baa.f90 and can find the module m_graze.mod, it can't seem to find the symbols for m_graze even though all the requisite information is present on the system for it to do so.
It would seem to be an easy matter of configuration to get the linker portion of ifort to find the missing pieces and put them together but I have no idea what magic words need to be entered where in the Photran UI to make this happen.
I confess an utter lack of interest and competence in C and the C build process and I'd rather avoid the diversion of creating libraries (.a or .so) unless that's the only way to make this work.
Ultimately, I'm looking for a pure Fortran solution to this problem so I can keep a single copy of the source code and don't have to manually maintain a pile of custom Makefiles.
So can this be done?
Apologies if this has already been documented somewhere; Google is only showing me simple build examples, how to create modules, and how to link with existing libraries. There don't seem to be (m)any examples of code reuse with modules that don't involve duplicating source code.
Edit
As respondents have pointed out, the .mod files are necessary but not sufficient; either object code (in the form of m_graze.o) or static or shared libraries must be specified during the linking phase. The .mod files describe the interface to the object code/library but both are necessary to build the final executable.
For an oversimplified toy problem such as this, that's sufficient to answer the question as posed.
In a larger project with more complex dependencies (in my case, 80+KLOC of F90 linking to the MKL version of LAPACK95), the IDE or toolchain may lack sufficient automatic or user-interface facilities to make sharing a single canonical set of source files a viable strategy. The choice seems to be between risking duplicate source files getting out of sync, giving up many of the benefits of an IDE (i.e. avoiding manual creation of make/CMake/SCons files), or, in all likelihood, both. While a revision control system and good code organization can help, it's clear that sharing a single canonical set of source files among projects is far from easy given the current state of Eclipse.
Some background which I suspect you already know: Typically (including ifort) compiling the source code for a Fortran module results in two outputs - a "mod" file that contains a description of the Fortran entities that the module defines that the compiler needs to find whenever it sees a USE statement for the module, and object code for the linker that implements the procedures and variable storage, etc., that the module defines.
Your first error (the one you solved) is because the compiler couldn't find the mod file.
The second error is because the linker hasn't been told about the object code that implements the stuff that was in the source file with the module. I'm not an Eclipse user by any means, but a brute force way of specifying that is just to add the object file (xxxxx/Debug/m_graze.o) as an additional linker option (Fortran Build > Settings, under Intel Fortran Linker > Command Line). (Other tool chains have explicit "additional object file" properties for their link stage - there may well be a better way of doing this for the Intel chain.)
For more involved examples you would typically create a library out of the shared code. That's not really C specific, the only Fortran aspect is that the libraries archive of object code needs to be provided alongside the mod files that the Fortran compiler generates.
Yes the object code must be provided. E.g., when you install libnetcdf-dev in Debian (apt-get install libnetcdf-dev), there is a /usr/include/netcdf.mod file that is included.
You can now use all netcdf routines in your Fortran code. E.g.,
program main
use netcdf
...
end
but you'll have link to the netcdf shared (or static) library, i.e.,
gfortran -I/usr/include/ main.f90 -lnetcdff
However, as user MSB mentioned the mod file can only be used by gfortran that comes with the distribution (apt-get install gfortran). If you want to use any other compiler (even a different version that you may have installed yourself) then you'll have to build netcdf yourself using that particular compiler.
So creating a library is not a bad solution.
Is it possible to extract a binary, to get the code that is behind the binary? With Class-dump you can see the implementation addresses, but is it possible to also see the code thats IN the implementation addresses? Is there ANY way to do it?
All your code compiles to single instructions, placed in the text section of your executable. The compiler is responsible for translating your higher level language to the processor specific instructions, which are simpler. Reverting this process would be nearly impossible, unless the code is quite simple. Some problems are ambiguity of statements, and the overall readability: local variables, for instance, will be nothing but an offset address.
If you want to read the disassembled code (the instructions of which the higher level code was compiled to) use this command in an executable:
otool -tV file
You can decompile (more accurately, disassemble) a binary and get it's assembly, but there is no way to get back the original Objective-C.
My curiosity begs me to ask why you want to do this!?
otx http://otx.osxninja.com/ is a good tool for symbolicating the otool based disassembly
It will handle both x86_64 and i386 disassembly.
and
Mach-O-Scope https://github.com/smorr/Mach-O-Scope is a a tool built on top of otx to dump it all into a sqlite3 database for browsing and annotating.
It won't give you the original source -- but it will get you pretty close providing you with the messages that are being sent around in methods.