janthorbecke / opensource Goto Github PK

Code for geophysical 3D/2D Finite Difference modelling, Marchenko algorithms, 2D/3D x-w migration and utilities.

License: Other

Makefile 0.46% C 64.06% Shell 10.40% PostScript 20.07% TeX 0.79% Fortran 0.76% Python 0.47% Gnuplot 0.01% C++ 1.91% MATLAB 0.27% HTML 0.01% CMake 0.06% Cuda 0.70% NASL 0.04%

finite-difference geophysics marchenko modeling wave-equation

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I'm new in using linux. I am trying to install your "opensource" codes following the installation guides given. However, I encountered some error. Hereby I attached the logs that i got after I type the "make" in the "opensource" directory.
error.txt

I have installed the MKL from https://software.intel.com/content/www/us/en/develop/tools/oneapi/base-toolkit/download.html

Am I missing some important steps?

threadAffinity missing and typo in fdelmodc.c (threadAfficity)

Hi Jan,

I've tried to compile your code, but I have encountered two issues:

in the fdelmodc/Makefile, there is a reference to threadAffinity.c, but the file does not exist (maybe you forgot to commit it);
in fdelmodc/fdelmodc.c, you use threadAfficity instead of threadAffinity (lines 15 and 508).

Cheers,
-Filippo

Intel MKL

Hey Guys!

I am new in GitHub, and also in Linux. I am gonna use this software in my thesis, and I am trying to run the code, but I have some problems with Intel MKL, saying:

/usr/bin/ld: cannot find -lmkl_gf_lp64
/usr/bin/ld: cannot find -lmkl_sequential
/usr/bin/ld: cannot find -lmkl_core

If you can help me, I will be appreciated.

Thanx

Make extrap error

Hello, Jan!

I got the following error when I making the program extrap on Ununtu18 with Intel CPU. However, I made it successfully on MacOS.

This error seems to be related to MKL, but other programs were successfully made.

How should I solve this problem?

Best regards.

cd main		; make 
make[1]: Entering directory '/home/wei/fdelmodc/extrap/main'
gcc -I/home/wei/fdelmodc/include -I. -O3 -ffast-math -fopenmp -DMKL -I/home/wei/intel/mkl/include -I/home/wei/intel/mkl/include/fftw  migr.c -L/home/wei/fdelmodc/lib -lgenfft -Wl,-rpath /home/wei/intel/mkl/lib/intel64 -Wl,--start-group -L/home/wei/intel/mkl/lib/intel64 -lmkl_gf_lp64 -lmkl_sequential -lmkl_core -Wl,--end-group -lpthread -lm -ldl -L/home/wei/fdelmodc/lib -lextrap2d  -lgenfft -lm  -o migr.tmp
/home/wei/fdelmodc/lib/libgenfft.a(cc1fft.o): In function `cc1fft':
cc1fft.c:(.text+0x68): undefined reference to `DftiFreeDescriptor'
cc1fft.c:(.text+0x7a): undefined reference to `DftiCreateDescriptor_s_1d'
cc1fft.c:(.text+0x87): undefined reference to `DftiErrorClass'
cc1fft.c:(.text+0x95): undefined reference to `DftiCommitDescriptor'
cc1fft.c:(.text+0xa2): undefined reference to `DftiErrorClass'
/home/wei/fdelmodc/lib/libgenfft.a(cc1fft.o): In function `Rcc1fft':
cc1fft.c:(.text+0x178): undefined reference to `DftiFreeDescriptor'
cc1fft.c:(.text+0x18a): undefined reference to `DftiCreateDescriptor_s_1d'
cc1fft.c:(.text+0x197): undefined reference to `DftiErrorClass'
cc1fft.c:(.text+0x1a5): undefined reference to `DftiCommitDescriptor'
cc1fft.c:(.text+0x1b2): undefined reference to `DftiErrorClass'
/home/wei/fdelmodc/lib/libgenfft.a(cc1fft.o): In function `cc1fft_':
cc1fft.c:(.text+0x288): undefined reference to `DftiFreeDescriptor'
cc1fft.c:(.text+0x29a): undefined reference to `DftiCreateDescriptor_s_1d'
cc1fft.c:(.text+0x2a7): undefined reference to `DftiErrorClass'
cc1fft.c:(.text+0x2b5): undefined reference to `DftiCommitDescriptor'
cc1fft.c:(.text+0x2c2): undefined reference to `DftiErrorClass'
/home/wei/fdelmodc/lib/libgenfft.a(cc1fft.o): In function `cc1fft':
cc1fft.c:(.text+0x53): undefined reference to `DftiComputeForward'
cc1fft.c:(.text+0xce): undefined reference to `DftiComputeBackward'
/home/wei/fdelmodc/lib/libgenfft.a(cc1fft.o): In function `Rcc1fft':
cc1fft.c:(.text+0x163): undefined reference to `DftiComputeForward'
cc1fft.c:(.text+0x1de): undefined reference to `DftiComputeBackward'
/home/wei/fdelmodc/lib/libgenfft.a(cc1fft.o): In function `cc1fft_':
cc1fft.c:(.text+0x273): undefined reference to `DftiComputeForward'
cc1fft.c:(.text+0x2ee): undefined reference to `DftiComputeBackward'
/home/wei/fdelmodc/lib/libgenfft.a(rc1fft.o): In function `rc1fft':
rc1fft.c:(.text+0x4a): undefined reference to `DftiComputeForward'
rc1fft.c:(.text+0x57): undefined reference to `DftiErrorClass'
rc1fft.c:(.text+0xc8): undefined reference to `DftiFreeDescriptor'
rc1fft.c:(.text+0xda): undefined reference to `DftiCreateDescriptor_s_1d'
rc1fft.c:(.text+0xe7): undefined reference to `DftiErrorClass'
rc1fft.c:(.text+0x105): undefined reference to `DftiSetValue'
rc1fft.c:(.text+0x112): undefined reference to `DftiErrorClass'
rc1fft.c:(.text+0x130): undefined reference to `DftiSetValue'
rc1fft.c:(.text+0x13d): undefined reference to `DftiErrorClass'
rc1fft.c:(.text+0x14f): undefined reference to `DftiCommitDescriptor'
rc1fft.c:(.text+0x15c): undefined reference to `DftiErrorClass'
rc1fft.c:(.text+0x174): undefined reference to `DftiErrorMessage'
rc1fft.c:(.text+0x1a4): undefined reference to `DftiErrorMessage'
rc1fft.c:(.text+0x1d4): undefined reference to `DftiErrorMessage'
rc1fft.c:(.text+0x204): undefined reference to `DftiErrorMessage'
rc1fft.c:(.text+0x234): undefined reference to `DftiErrorMessage'
/home/wei/fdelmodc/lib/libgenfft.a(rc1fft.o):rc1fft.c:(.text+0x265): more undefined references to `DftiErrorMessage' follow
/home/wei/fdelmodc/lib/libgenfft.a(crmfft.o): In function `crmfft':
crmfft.c:(.text+0x1e3): undefined reference to `DftiComputeBackward'
crmfft.c:(.text+0x3f3): undefined reference to `DftiErrorClass'
crmfft.c:(.text+0x42c): undefined reference to `DftiFreeDescriptor'
crmfft.c:(.text+0x43e): undefined reference to `DftiCreateDescriptor_s_1d'
crmfft.c:(.text+0x44b): undefined reference to `DftiErrorClass'
crmfft.c:(.text+0x46e): undefined reference to `DftiSetValue'
crmfft.c:(.text+0x47b): undefined reference to `DftiErrorClass'
crmfft.c:(.text+0x49e): undefined reference to `DftiSetValue'
crmfft.c:(.text+0x4ab): undefined reference to `DftiErrorClass'
crmfft.c:(.text+0x4c2): undefined reference to `DftiCommitDescriptor'
crmfft.c:(.text+0x4d1): undefined reference to `DftiErrorClass'
collect2: error: ld returned 1 exit status
Makefile:26: recipe for target 'migr' failed
make[1]: *** [migr] Error 1
make[1]: Leaving directory '/home/wei/fdelmodc/extrap/main'
Makefile:4: recipe for target 'all' failed
make: *** [all] Error 2

Trying to run acoustic SH4

Dear Sir,

We are trying to run acousticSH4( ) for SH wave modeling. But the output results shows zero and nan values.
Kindly help in correcting the execution.
Attached herewith is the snap of input parameters.

Issue with trace headers after run modeling

Dear Sir Jan,

I tried to run your model.sh example in ~/OpenSource/marchenko3D/demo/marchenko3D/oneD in my machine.

The output of cp3d.su that I obtained looks like this:

Which is I think not really correct. The numbers are weird.

I noticed these messages during the modeling is executed:

Am I missing the requirements to run the modeling?

Regards,
Mirumuz

Mistake cc1fft.c

Hello Jan!!
I Would like to use Marchenko Migration in Colombia Complex Area, it is about the University Project, I followed the instruction but had the next mistake.
My Processor is AMD and OS: Ubuntu18
Thanks Regards

make
make[1]: Entering directory '/home/zignal/OpenSource-master/FFTlib'
mkdir -p /home/zignal/OpenSource-master/lib
mkdir -p /home/zignal/OpenSource-master/include
cp -rp genfft.h /home/zignal/OpenSource-master/include/genfft.h
gcc -c -I/home/zignal/OpenSource-master/include -I. -O3 -ffast-math -fopenmp -DMKL -I/include -I/include/fftw -I/home/zignal/OpenSource-master/zfp/include cc1fft.c

. cc1fft.c:3:10: fatal error: mkl_dfti.h: No such file or directory**

include "mkl_dfti.h"
compilation terminated.
/Make_include:124: recipe for target '/home/zignal/OpenSource-master/lib/libgenfft.a(cc1fft.o)' failed
make[1]: *** [/home/zignal/OpenSource-master/lib/libgenfft.a(cc1fft.o)] Error 1
make[1]: Leaving directory '/home/zignal/OpenSource-master/FFTlib'
Makefile:4: recipe for target 'all' failed
make: *** [all] Error 2

Little Bug

Hello,Thorbecke, I find a little bug in Code "fdacrtmc" ,in file "boundaries.c" ,The PML in acoustic scheme has a bug.The location is line 293,code is "for(iz=mod->iePz,ipml=0 ; izieZzb ; iz++) " ,Max lose "ipml++",and it causes a false reflection in the lower right corner of the simulated area.

            A Marchenko learner from China,thanks!!!

A compilation error using gfortran 11.2.0

Dear sir,
I tried to install your code on Ubuntu 22.04. The default version of gcc and gfortran is 11.2.0. And I get this error message when make the MDD:

gfortran ......
/usr/bin/ld: deconvolve.o:(.bss+0x0): multiple definition of `cB'; mdd.o:(.bss+0x0): first defined here
collect2: error: ld returned 1 exit status

I noticed when I used gfortran 4.8.5 to complie it, everything is fine. So maybe the new version of gfortran has stricter syntax.

Then I check the code and find there are two same variable definitions in MDD/deconvolve.c and MDD/mdd.c

I change the variable name in deconvolve.c to solve the problem.
I want to know if this change will affect the operation of the program. If it doesn't, I suggest you to fix this bug.

Installation Error

I am trying to install OpenSource on my Mac M1. But I'm facing an issue where some gfortran symbols are said to be undefined. I have installed gfortran and it seems to be working fine.
error.txt

Installation problem-NetCDF

Hi,
After installing the software, I try the ./fdelmodc_plane.scr. Error comes:
file_base defined for NetCDF output, but code not compiled for NetCDF support: recompile with -D_NETCDF.

It seems like I need to recompile the codes. Does anyone know how to modify the makefile?
Thx!

janthorbecke / opensource Goto Github PK

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