This project forked from adaptiveoptics-org/cfits
Multi-purpose Imaging Libraries toolKit (milk)
Home Page: https://milk-org.github.io/milk/
License: GNU General Public License v3.0
Description
If compiler=pgcc (version 18.4), cmake can't find (n)curses library.
Strangely, this does not occur if compiler=gcc (version 7.2)
Fix:
Added in file /usr/local/share/cmake-3.11/Modules/FindCurses.cmake, at top of file:
set(CURSES_LIBRARY "/usr/lib/x86_64-linux-gnu/libncurses.so")
set(CURSES_INCLUDE_PATH "/usr/include")
Not sure if this is an issue with our cmake files...
IMPORTANT: I am proposing the following changes to the data structure in milk (+cacao, coffee). Please read carefully and let me know if you disagree.
[1] Remove default attribute ((packed)) for IMAGE_METADATA, IMAGE, EVENT_UI8_UI8_UI16_UI8, and EVENT_UI8_UI8_UI16_UI8.
I propose to enable these with an option specified at compile time, but have the default behavior to not pack the data.
Why ?
Code will run faster and be more portable to non gcc compilers. Compiler can do more optimization.
I ran into a nasty memory alignment bug when compiling with pgcc with -fast option which I do not yet fully understand, but clearly due to this packing. Removing the packing solved the issue.
Read this (pointed out by Frantz):
https://stackoverflow.com/questions/8568432/is-gccs-attribute-packed-pragma-pack-unsafe
and this (pointed out by Jared):
http://www.catb.org/esr/structure-packing/
Why not ?
Very small loss in memory usage efficiency.
Possible impact on low-level reading of fields in structure as pointer offsets may be compiler-optimized (note: this should be addressed by other approaches, and milk could print out pointer offsets to a file for others to read)
[2] Simplify data, and new locations for definition/declaration
data is currently a variable of type DATA (using typedef to a structure). Since we only have one instance of this DATA type variable, I propose to get rid of the typedef. I also propose to declare the data variable as extern in CLIcore.h which is already included in all source files requiring its use.
The proposed change would have in CLIcore.h:
struct DATA { ....};
extern struct DATA data;
data will be defined in CLImain.c:
struct DATA data;
.. and will no longer need to be declared in other files (part of included CLIcore.h)
[3] Implement static allocation of data.image and data.variable arrays, provide use with option to set smaller initial image and variable array sizes.
The current scheme is to have a dynamic allocation (default: 5000 instances) and grow it with reallocs when more needed. This works, but is not optimal is speed (compiler can better optimize with statically allocated arrays), and in some cases, we need to support smaller sized arrays for faster I/O.
I propose to :
GIT can provide tools to check / lint the code before creating a commit. We are using it in our simulation project COMPASS and I find it very useful.
So, I have several questions regarding hooks:
If you want, I can put it in my branch and try it before adopting it (or not)
Cheers,
Arnaud
Wondering how to cleanly integrate doxygen documentation with git workflow.
When running doxygen within a branch (dev or master), content of ./html/ directory is rewritten
This interferes with commits/push/merge
Is it possible to have html directory only part of master branch ? (this is different from git practices...)
Here's what I'm seeing
/bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -std=gnu11 -fopenmp -o milk milk-CLImain.o CommandLineInterface/milk-CLIcore.o CommandLineInterface/milk-calc_bison.o CommandLineInterface/milk-calc_flex.o cudacomp/libcudacomp.la linARfilterPred/liblinarfilterpred.la psf/libpsf.la img_reduce/libimgreduce.la image_format/libimageformat.la ZernikePolyn/libzernikepolyn.la image_basic/libimagebasic.la image_filter/libimagefilter.la image_gen/libimagegen.la linopt_imtools/liblinoptimtools.la statistic/libstatistic.la info/libinfo.la fft/libfft.la kdtree/libkdtree.la COREMOD_arith/libcoremodarith.la COREMOD_memory/libcoremodmemory.la COREMOD_iofits/libcoremodiofits.la COREMOD_tools/libcoremodtools.la 00CORE/lib00core.la ImageStreamIO/libimagestreamio.la -lgsl -lgslcblas -lrt -lgomp -lfftw3 -lfftw3f -lncurses -lreadline -lcfitsio -ldl -lm -lpthread
libtool: link: gcc -g -O2 -std=gnu11 -fopenmp -o .libs/milk milk-CLImain.o CommandLineInterface/milk-CLIcore.o CommandLineInterface/milk-calc_bison.o CommandLineInterface/milk-calc_flex.o cudacomp/.libs/libcudacomp.so linARfilterPred/.libs/liblinarfilterpred.so psf/.libs/libpsf.so img_reduce/.libs/libimgreduce.so image_format/.libs/libimageformat.so ZernikePolyn/.libs/libzernikepolyn.so image_basic/.libs/libimagebasic.so image_filter/.libs/libimagefilter.so image_gen/.libs/libimagegen.so linopt_imtools/.libs/liblinoptimtools.so statistic/.libs/libstatistic.so info/.libs/libinfo.so fft/.libs/libfft.so kdtree/.libs/libkdtree.so COREMOD_arith/.libs/libcoremodarith.so COREMOD_memory/.libs/libcoremodmemory.so COREMOD_iofits/.libs/libcoremodiofits.so COREMOD_tools/.libs/libcoremodtools.so 00CORE/.libs/lib00core.so ImageStreamIO/.libs/libimagestreamio.so -lgsl -lgslcblas -lrt -lgomp -lfftw3 -lfftw3f -lncurses -lreadline -lcfitsio -ldl -lm -lpthread -fopenmp -Wl,-rpath -Wl,/opt/MagAOX/source/milk/lib
CommandLineInterface/milk-CLIcore.o: In function `functionparameter_CTRLscreen_cli':
/opt/MagAOX/source/milk/src/CommandLineInterface/CLIcore.c:570: undefined reference to `functionparameter_CTRLscreen'
CommandLineInterface/milk-CLIcore.o: In function `main_init':
/opt/MagAOX/source/milk/src/CommandLineInterface/CLIcore.c:1618: undefined reference to `processinfo_CTRLscreen'
/opt/MagAOX/source/milk/src/CommandLineInterface/CLIcore.c:1627: undefined reference to `streamCTRL_CTRLscreen'
COREMOD_memory/.libs/libcoremodmemory.so: undefined reference to `processinfo_WriteMessage'
COREMOD_memory/.libs/libcoremodmemory.so: undefined reference to `processinfo_exec_start'
COREMOD_memory/.libs/libcoremodmemory.so: undefined reference to `processinfo_exec_end'
COREMOD_memory/.libs/libcoremodmemory.so: undefined reference to `processinfo_cleanExit'
COREMOD_memory/.libs/libcoremodmemory.so: undefined reference to `processinfo_SIGexit'
COREMOD_memory/.libs/libcoremodmemory.so: undefined reference to `processinfo_shm_create'
collect2: error: ld returned 1 exit status
make[3]: *** [Makefile:522: milk] Error 1
make[3]: Leaving directory '/opt/MagAOX/source/milk/src'
make[2]: *** [Makefile:635: all-recursive] Error 1
make[2]: Leaving directory '/opt/MagAOX/source/milk/src'
make[1]: *** [Makefile:418: all] Error 2
make[1]: Leaving directory '/opt/MagAOX/source/milk/src'
make: *** [Makefile:379: all-recursive] Error 1
Here's my build script:
git clone --recursive https://github.com/milk-org/milk milk
cd ./milk
git checkout dev
autoreconf -i
./configure
make
make install
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