I am programming in Fortran 90 using GFortran and I'm having troubles with Modules. When I compile the code below, I get the following error:
Derivatives.f90:7.16:
Included at C:\Users\dchalhub\Dropbox\Doutorado\#Tese\New folder\main.f90:1:
Use Mesh
1
Fatal Error: Can't open module file 'mesh.mod' for reading at (1): No such file or directory
gfortran.exe: Internal error: Aborted (program f951)
Please submit a full bug report.
See <http://gcc.gnu.org/bugs.html> for instructions.
So, the 'mesh.mod' file is not created.
But when I remove the first two lines: 'include 'Derivatives.f90'' and 'include 'Poisson.f90'' the module is created without any problems.
After the mod file is created, I put back the first two lines, compile the code again and it works perfectly.
include 'Derivatives.f90'
include 'Poisson.f90'
!**************************************************************
MODULE MESH
IMPLICIT NONE
INTEGER :: IMAX,JMAX,NMAX
REAL(8), ALLOCATABLE :: XD(:),YD(:),FX(:,:),FY(:,:)
REAL(8) :: PI,E,DX,DY,H,L,RHO,MU
PARAMETER (PI = ACOS(-1.D0))
PARAMETER (E = 2.71828182845904523536028747135266249775724709369995)
END MODULE MESH
!**************************************************************
!**************************************************************
!*********** Lid-driven Cavity Program*************************
!**************************************************************
program Cavity
Use Mesh
implicit none
End program Cavity
I don't know why but there is something wrong with compiling multiple files with modules.
Does any one know what should I do to make it work properly?
Related
I'm really lost on how to actually use multiple files in Coq. I was trying to follow these directions.
I have two files.
src/a.v:
Definition bar: nat := 1.
src/b.v:
Require Import a.
Definition foo := bar.
I attempt to compile as such:
coqc -R src "" src/a.v src/b.v
I get the following error:
user#machine:~/code/coq$ coqc -R src "" src/a.v src/b.v
While loading initial state:
Loading file /home/user/code/coq/src/.b.aux: aux file name mismatch
I can't find any clear information on how you actually compile with multiple files
I recommend you perform two calls to coqc, first with a then with b. Having multiple files in the argument command line is actually not supported [we will improve the interface in next versions as to warn about this]
Using Cudafy version 1.29, which can be downloaded from here
I am executing the examples that are found in the install folder CudafyV1.29\CudafyByExample\
Specifically, "chapter 3" example that begins line 42 of program.cs calls the following:
simple_kernel.Execute();
which is this:
public static void Execute()
{
CudafyModule km = CudafyTranslator.Cudafy(); // <--exception thrown!
GPGPU gpu = CudafyHost.GetDevice(CudafyModes.Target, CudafyModes.DeviceId);
gpu.LoadModule(km);
gpu.Launch().thekernel(); // or gpu.Launch(1, 1, "kernel");
Console.WriteLine("Hello, World!");
}
The indicated line throws this exception:
Compilation error: CUDAFYSOURCETEMP.cu
'C:\Program' is not recognized as an internal or external command,
operable program or batch file. .
Which is immediately obvious that the path has spaces and the programmer did not double quote or use ~ to make it operational.
So, I did not write this code. And I cannot step through the sealed code contained within CudafyModule km = CudafyTranslator.Cudafy();In fact I don't even know the full path that is causing the exception, it is cut-off in the exception message.
Does anyone have a suggestion for how to fix this issue?
Update #1: I discovered where CUDAFYSOURCETEMP.cu lives on my computer, here it is:
C:\Users\humphrt\Desktop\Active Projects\Visual Studio
Projects\CudafyV1.29\CudafyByExample\bin\Debug
...I'm still trying to determine what the program is looking for along the path to 'C:\Program~'.
I was able to apply a workaround to bypass this issue. The workaround is to reinstall all components of cudafy in to folders with paths with no ' ' (spaces). My setup looks like the below screenshot. Notice that I also installed the CUDA TOOLKIT from NVIDIA in the same folder - also with no spaces in folder names.
I created a folder named "C:\CUDA" and installed all components within it, here is the folder structure:
This question already has an answer here:
Reading data from matlab files into C
(1 answer)
Closed 7 years ago.
I have to import a MAT-file in a fortran program. I followed the example file but I am facing some problems while linking. The compilation happens fine.
Minimal code:
#include "fintrf.h"
PROGRAM main
USE ssa
USE dmotifs
USE param
IMPLICIT NONE
! MAT-FILE Declarations !
INTEGER matOpen, matGetDir
INTEGER matGetVariableInfo
INTEGER mp, dir, adir(100), pa
INTEGER mxGetM, mxGetN, matClose
INTEGER ndir, i, clstat
CHARACTER*32 names(100)
!===========================!
if(all(fnames(:)%fn .NE. argfun)) then
write(*,*) "No such motif: ",argfun
write(*,*) "Input format-> main <motifname>"
stop
else
fin=fchton(argfun)
y0=nM2m*analys(p,argfun)
! ==> OPEN MAT-file <== !
mp=matOpen('./PRMS_lxr_29Apr15.mat','r')
if (mp .eq. 0) then
write(6,*) "Can't open MAT-file"
stop
end if
dir = matgetdir(mp, ndir)
if (dir .eq. 0) then
write(6,*) "Can't read MAT-file-directory."
stop
endif
call mxCopyPtrToPtrArray(dir, adir, ndir)
do 20 i=1,ndir
call mxCopyPtrToCharacter(adir(i), names(i), 32)
20 continue
write(6,*) 'Directory of Mat-file:'
do 30 i=1,ndir
write(6,*) names(i)
30 continue
write(6,*) 'Getting Header info from first array.'
pa = matGetVariableInfo(mp, names(1))
write(6,*) 'Retrieved ', names(1)
write(6,*) ' With size ', mxGetM(pa), '-by-', mxGetN(pa)
call mxDestroyArray(pa)
clstat=matClose(mp)
end if
END PROGRAM main
I am using gfortran 4.8.3 for compiling+linking using the default command:
gfortran main.f90 dmotifs.o param.o ssa.o -o main
This code compiles fine (without linking) when I do not include: #include "finitrf.h", otherwise the compiler says
Warning: main.f90:1: Illegal preprocessor directive
I tried renaming finitrf.h to finitrf.f90 but it did not make any difference. Nonetheless during linking I am getting these errors:
main.f90:(.text+0x3ea): undefined reference to `matopen_'
main.f90:(.text+0x487): undefined reference to `matgetdir_'
main.f90:(.text+0x52b): undefined reference to `mxcopyptrtoptrarray_'
main.f90:(.text+0x583): undefined reference to `mxcopyptrtocharacter_'
main.f90:(.text+0x71b): undefined reference to `matgetvariableinfo_'
main.f90:(.text+0x804): undefined reference to `mxgetm_'
main.f90:(.text+0x855): undefined reference to `mxgetn_'
main.f90:(.text+0x89c): undefined reference to `mxdestroyarray_'
main.f90:(.text+0x8b0): undefined reference to `matclose_'
collect2: error: ld returned 1 exit status
Do I need a makefile or add additional arguments in the compile command?
EDIT:
I added the -cpp option and that eliminates the problem of Illegal preprocessor directive
Now when I am compiling with paths to matlab external components (where finitf.h) is, I am still getting the same error.
gfortran main.f90 dmotifs.o param.o ssa.o -I/usr/local/matlab2008a/extern/include -L/usr/local/matlab2008a/extern/lib -cpp -o main
If I provide library path to /usr/local/matlab2008a/bin/glnxa64 that contains other matlab libraries including libmat.so, I still get the same errors.
For lower case file extensions *.f90 or *.f the pre-processor is typically deactivated. To enable that, either rename the (main) file to have a capital extension *.F90 or *.F, or provide the corresponding command-line option (-cpp for gfortran, -fpp for ifort).
Assuming the missing subroutines/functions are actually declared in fintrf.h, this should solve your problem.
You should additionally tell the compiler to link against the libraries containing the Matlab functions.
As pointed out by Alexander Vogt, the compiler requires -cpp option for the pre-processor to recognize the header file and not to treat it as illegal.
Linking requires finitrf.h which is usually located in the <matlabroot>/extern/include and the essential libraries are present in <matlabroot>/bin/<arch>/.
But just specifying this does not work and specification of the exact matlab library seems essential; these are libmat.so and libmx.so.
These libraries are in turn dependent on other libraries so another flag is required to set the rpath.
Finally it works with following command:
gfortran main.f90 dmotifs.o param.o ssa.o -I/usr/local/matlab2008a/extern/include -L/usr/local/matlab2008a/bin/glnxa64 -cpp -o main -lmat -lmx -Wl,-rpath /usr/local/matlab2008a/bin/glnxa64/
or in general
gfortran program.f90 -I<matlabroot>/extern/include -L<matlabroot>/bin/<arch> -cpp -lmat -lmx -Wl, -rpath <matlabroot>/bin/<arch> -o program.out
Also see this post that is about the same problem in C.
everyone!
I'm trying to parallelize an algorithm that uses mex files from mexopencv (KNearest.m, KNearest_.mexw32).
The program is based vlfeat (vlsift.mex32) + mexopencv (KNearest.m and KNearest_.mexw32).I classify descriptors obtained from images.
All the code is located on the fileshare
\\ LAB-07 \ untitled \ DISTRIB \ (this is the program code)
\\ LAB-07 \ untitled \ + cv (mexopencv)
When I run the program with matlabpool close everything works well.
Then I make matlabpool open (2 computers on 2 cores each. ultimately 4 worker, but now I use for testing only 2 workers on the computer and run the program which)
PathDependencises from fileshare -> \LAB-07\untitled\DISTRIB\ , \LAB-07\untitled+cv
Before parfor loop I train classifier on the local machine
classifiers = cv.KNearest
classifiers.train(Descriptors',Labels','MaxK',1)
Then run parfor
descr=vlsift(img);
PredictClasses = classifiers.predict(descr');
Error
Error in ==> KNearest>KNearest.find_nearest at 173
Invalid MEX-file '\\LAB-07\untitled\+cv\private\KNearest_.mexw32':
The specified module could not be found.
That is KNearest.m finds, but no KNearest_.mexw32. Because KNearest_.mexw32 located in private folder, I changed the code KNearest.m (everywhere where it appeal KNearest_ () changed to cv.KNearest_ (). Example: this.id = сv.KNearest_ ()) and placed in a folder with KNearest_.mexw32 KNearest.m. As a result, get the same error
Immediately after matlabpool open file search on workers
pctRunOnAll which ('KNearest.m')
'KNearest.m' not found.
'KNearest.m' not found.
'KNearest.m' not found.
pctRunOnAll which ('KNearest_.mexw32')
'KNearest_.mexw32' not found.
'KNearest_.mexw32' not found.
'KNearest_.mexw32' not found.
after cd \LAB-07\untitled+cv
pctRunOnAll which ('KNearest.m')
\\LAB-07\untitled\+cv\KNearest.m
\\LAB-07\untitled\+cv\KNearest.m % cv.KNearest constructor
\\LAB-07\untitled\+cv\KNearest.m
>> pctRunOnAll which ('KNearest_.mexw32')
\\LAB-07\untitled\+cv\KNearest_.mexw32
\\LAB-07\untitled\+cv\KNearest_.mexw32
\\LAB-07\untitled\+cv\KNearest_.mexw32
I ran and FileDependecies, but the same result.
I do not know this is related or not, I display during the execution of the program classifiers
after training and before parfor
classifiers =
cv.KNearest handle
Package: cv
Properties:
id: 5
MaxK: 1
VarCount: 128
SampleCount: 9162
IsRegression: 0
Methods, Events, Superclasses
Within parfor before classifiers.predict
classifiers =
cv.KNearest handle
Package: cv
Properties:
id: 5
I tested the file cvtColor.mexw32. I left in a folder only 2 files cvtColor.mexw32 and vl_sift
parfor i=1:2
im1=imread('Copy_of_start40.png');
im_vl = im2single(rgb2gray(im1));
desc=vl_sift(im_vl);
im1 = cvtColor(im1,'RGB2GRAY');
end
The same error, and vl_sift work, cvtColor no...
If the worker machines can see the code in your shared filesystem, you should not need FileDependencies or PathDependencies at all. It looks like you're using Windows. It seems to me that the most likely problem is file permissions. MDCS workers running under a jobmanager on Windows by default run not using your own account (they run using the "LocalSystem" account I think), and so may well simply not have access to files on a shared filesystem. You could try making sure your code is world-readable.
Otherwise, you can add the files to the pool by using something like
matlabpool('addfiledependencies', {'\\LAB-07\untitled\+cv'})
Note that MATLAB interprets directories with a + in as defining "packages", not sure if this is intentional in your case.
EDIT
Ah, re-reading your original post, and your comments below - I suspect the problem is that the workers cannot see the libraries on which your MEX file depends. (That's what the "Invalid MEX-file" message is indicating). You could use http://www.dependencywalker.com/ to work out what are the dependencies of your MEX file, and make sure they're available on the workers (I think they need to be on %PATH%, or in the current directory).
Edric thanks. There was a problem in the PATH for parfor. With http://www.dependencywalker.com/ looked missing files and put them in a folder +cv. Only this method works in parfor.
But predict in parfor gives an error
PredictClasses = classifiers.predict(descr');
??? Error using ==> parallel_function at 598
Error in ==> KNearest>KNearest.find_nearest at 173
Unexpected Standard exception from MEX file.
What() is:..\..\..\src\opencv\modules\ml\src\knearest.cpp:365: error: (-2) The search
tree must be constructed first using train method
I solved this problem by calling each time within parfor train
classifiers = cv.KNearest
classifiers.train(Descriptors',Labels','MaxK',1)
But it's an ugly solution :)
I tried installing Pygame version 1.9.1release for PyPy on my Mac OSX Lion. I ran pypy config.py first with pypy setup.py install. I added the config to the installation process since I saw that it was trying to configure with normal python (which installs correctly, but causes import errors). Durring the installation process, there are many warnings such as:
src/overlay.c:44:5: warning: implicit declaration of function 'PyObject_Free' is invalid in C99 [-Wimplicit-function-declaration]
PyObject_Free ((PyObject*)self);
^
But it also provided me with 2 similar errors:
In file included from src/scale_mmx.c:33:
src/scale_mmx64.c:424:27: error: invalid instruction mnemonic 'movsxl'
asm __volatile__( " /* MMX code for inner loop of X bilinear filter */ "
^
<inline asm>:1:191: note: instantiated into assembly here
/* MMX code for inner loop of X bilinear filter */ movl -36(%rbp), %ecx; pxor %mm0, %mm0; 1: movsxl (%rdi), ...
^~~~~~
In file included from src/scale_mmx.c:33:
src/scale_mmx64.c:499:27: error: invalid instruction mnemonic 'movsxl'
asm __volatile__( " /* MMX code for inner loop of X bilinear filter */ "
^
<inline asm>:1:191: note: instantiated into assembly here
/* MMX code for inner loop of X bilinear filter */ movl -36(%rbp), %ecx; pxor %mm0, %mm0; 1: movsxl (%rdi), ...
^~~~~~
2 errors generated.
It seems rather silly to me that PyPy got stuck at a line that generates what seems to be a block comment in C. And why its encapsulated the comment in asm and volatile is beyond me. But this is the code that was provided to me and works in regular python. So is this a bug? Or am I missing something?
Chances are PyPy has some #defines different than CPython (for good or bad reasons) and pygame chooses to use something else (based on a badly thought out #else with implicit assumptions) that tries to compile invalid C. I'm just guessing though, you would need to follow why and how the same code is/is not compiled on CPython.