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Merged
merged 89 commits into from
Sep 28, 2025
Merged

V1.1.4 #39

merged 89 commits into from
Sep 28, 2025

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@mahmoudElkarargyBS
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Sameh M. Abdulah and others added 30 commits November 23, 2023 14:51
add the pow_exp kernel and tested
de62bfa
@mahmoudElkarargyBS
all fixes
b1c0165
@mahmoudElkarargyBS
resolve threads plus some modifications
d8cefec
@mahmoudElkarargyBS
Fix cuda
eea866b
@mahmoudElkarargyBS
fix for linking cuda
6884d5c
@mahmoudElkarargyBS
fix: hicma modifactions
cd7cda3
@mahmoudElkarargyBS
try fixing Jenkines
f72d63c
@mahmoudElkarargyBS
Adding R structure
210c06b
@mahmoudElkarargyBS
fix:add doxygen in Jenkines
5b604ba
add test file for pow-exp kernel
b1f0fbf
@mahmoudElkarargyBS
test with -fpic
b5d530e
@mahmoudElkarargyBS
some modifications for HiCMA
957dd0c
@mahmoudElkarargyBS
updates
fe1f893
@mahmoudElkarargyBS
try 2 gpu devices
6a61410
@mahmoudElkarargyBS
back to starsh
346a0d8
@mahmoudElkarargyBS
a potential fix to doxygen
2d3bc17
@mahmoudElkarargyBS
roll back
5446c76
@mahmoudElkarargyBS
test Rcpp
da8ad1f
@mahmoudElkarargyBS
Fix Jenkines
2ea149e
@mahmoudElkarargyBS
fix errors
6481324
@mahmoudElkarargyBS
Updated in design
038e923
@mahmoudElkarargyBS
updates
836ccbc
@mahmoudElkarargyBS
all release issue without src checks
21e826b
@mahmoudElkarargyBS
Merge pull request #1 from ecrc/FIX-release-issue-MK
f56153c 
Version 1.0.1
@mahmoudElkarargyBS
merge devel
18564f6
@mahmoudElkarargyBS
Merge pull request #2 from ecrc/kernel/pow-exp
c3fd36a 
add the pow_exp kernel and tested
@mahmoudElkarargyBS
merge devel
ad24449
@mahmoudElkarargyBS
adding MakeFile
b4c6e7d
@mahmoudElkarargyBS
Updated MPI
f4e7e80
@mahmoudElkarargyBS
Documentation
96d6dde
mahmoudElkarargyBS and others added 21 commits May 10, 2024 03:05
@mahmoudElkarargyBS
Ft test mpi mk (#6)
1864818 
* solve multi thread issue in MPI

* Fix MPI tests with chameleon

* Fixed HiCMA with MPI

* update license
@mahmoudElkarargyBS
minior cleanings (#7)
fd721cd
@mahmoudElkarargyBS
v1.1.0 (#4) (#8)
aa56c1c 
* add the pow_exp kernel and tested

* all fixes

* resolve threads plus some modifications

* Fix cuda

* fix for linking cuda

* fix: hicma modifactions

* try fixing Jenkines

* Adding R structure

* fix:add doxygen in Jenkines

* add test file for pow-exp kernel

* test with -fpic

* some modifications for HiCMA

* updates

* try 2 gpu devices

* back to starsh

* a potential fix to doxygen

* roll back

* test Rcpp

* Fix Jenkines

* fix errors

* Updated in design

* updates

* all release issue without src checks

* adding MakeFile

* Updated MPI

* Documentation

* fix examples tests

* modeling takes pointers

* example for read and write data

* fix: typpo in Initialize

* fix passing numbers of theta

* fix: performance of gsl

* fix: GPU support

* fix:mspe

* updated devel

* R branch init

* tests:add r tests

* fix tests

* bug: in tlr

* fix:tlr

* fix Jenkines

* fix: Jenkines in Documentation

* minior updates

* huge refactoring

* full R

* potential for tlr issue

* updates in heavy tests

* a fix for gpu in gaussian kernels

* smalling tlr size

* update sizes of heavy_tests

* smalling size for gpu

* minior changes

* Huge refactoring in docs

* resolve threads

* fix MPI

* resolve thread

* updated R documentation

* documentation and hardware changes

* finalized documentations

* minior change in Hardware

* Ft test mpi mk (#6)

* solve multi thread issue in MPI

* Fix MPI tests with chameleon

* Fixed HiCMA with MPI

* update license

* minior cleanings (#7)

---------

Co-authored-by: Sameh M. Abdulah <abdullsm@kw60194.kaust.edu.sa>
Co-authored-by: Mahmoud Karargy <x_karargma@almaha.kaust.edu.sa>
@mahmoudElkarargyBS
Fix P & Q
3fce527
@mahmoudElkarargyBS
updates in R (#9)
e459c18
@mahmoudElkarargyBS
resolve conflicts
58197b0
@mahmoudElkarargyBS
Fix error in R
733723d
@mahmoudElkarargyBS
Fix using of openblas (#16)
f995a5f
@mahmoudElkarargyBS
resolve conflicts
bd6fd82
@mahmoudElkarargyBS
Update main (#19)
0cdb463 
* V1.1.1 (#15)

* add the pow_exp kernel and tested

* all fixes

* resolve threads plus some modifications

* Fix cuda

* fix for linking cuda

* fix: hicma modifactions

* try fixing Jenkines

* Adding R structure

* fix:add doxygen in Jenkines

* add test file for pow-exp kernel

* test with -fpic

* some modifications for HiCMA

* updates

* try 2 gpu devices

* back to starsh

* a potential fix to doxygen

* roll back

* test Rcpp

* Fix Jenkines

* fix errors

* Updated in design

* updates

* all release issue without src checks

* adding MakeFile

* Updated MPI

* Documentation

* fix examples tests

* modeling takes pointers

* example for read and write data

* fix: typpo in Initialize

* fix passing numbers of theta

* fix: performance of gsl

* fix: GPU support

* fix:mspe

* updated devel

* R branch init

* tests:add r tests

* fix tests

* bug: in tlr

* fix:tlr

* fix Jenkines

* fix: Jenkines in Documentation

* minior updates

* huge refactoring

* full R

* potential for tlr issue

* updates in heavy tests

* a fix for gpu in gaussian kernels

* smalling tlr size

* update sizes of heavy_tests

* smalling size for gpu

* minior changes

* Huge refactoring in docs

* resolve threads

* fix MPI

* resolve thread

* updated R documentation

* documentation and hardware changes

* finalized documentations

* minior change in Hardware

* Ft test mpi mk (#6)

* solve multi thread issue in MPI

* Fix MPI tests with chameleon

* Fixed HiCMA with MPI

* update license

* minior cleanings (#7)

* v1.1.0 (#4) (#8)

* add the pow_exp kernel and tested

* all fixes

* resolve threads plus some modifications

* Fix cuda

* fix for linking cuda

* fix: hicma modifactions

* try fixing Jenkines

* Adding R structure

* fix:add doxygen in Jenkines

* add test file for pow-exp kernel

* test with -fpic

* some modifications for HiCMA

* updates

* try 2 gpu devices

* back to starsh

* a potential fix to doxygen

* roll back

* test Rcpp

* Fix Jenkines

* fix errors

* Updated in design

* updates

* all release issue without src checks

* adding MakeFile

* Updated MPI

* Documentation

* fix examples tests

* modeling takes pointers

* example for read and write data

* fix: typpo in Initialize

* fix passing numbers of theta

* fix: performance of gsl

* fix: GPU support

* fix:mspe

* updated devel

* R branch init

* tests:add r tests

* fix tests

* bug: in tlr

* fix:tlr

* fix Jenkines

* fix: Jenkines in Documentation

* minior updates

* huge refactoring

* full R

* potential for tlr issue

* updates in heavy tests

* a fix for gpu in gaussian kernels

* smalling tlr size

* update sizes of heavy_tests

* smalling size for gpu

* minior changes

* Huge refactoring in docs

* resolve threads

* fix MPI

* resolve thread

* updated R documentation

* documentation and hardware changes

* finalized documentations

* minior change in Hardware

* Ft test mpi mk (#6)

* solve multi thread issue in MPI

* Fix MPI tests with chameleon

* Fixed HiCMA with MPI

* update license

* minior cleanings (#7)

---------

Co-authored-by: Sameh M. Abdulah <abdullsm@kw60194.kaust.edu.sa>
Co-authored-by: Mahmoud Karargy <x_karargma@almaha.kaust.edu.sa>

* Fix P & Q

* updates in R (#9)

* Fix error in R

* Fix using of openblas (#16)

---------

Co-authored-by: Sameh M. Abdulah <abdullsm@kw60194.kaust.edu.sa>
Co-authored-by: Mahmoud Karargy <x_karargma@almaha.kaust.edu.sa>

* V1.1.2 (#17)

* Fixed cmake installation and add  requirements in ReadME

---------

Co-authored-by: Sameh M. Abdulah <abdullsm@kw60194.kaust.edu.sa>
Co-authored-by: Mahmoud Karargy <x_karargma@almaha.kaust.edu.sa>
@mahmoudElkarargyBS
Fix for zero values in locations (#20)
a4df6cf
@mahmoudElkarargyBS
update devel (#21)
a090ab2
@mahmoudElkarargyBS @SAbdulah
Fix tlr in R (#24)
eba9f5e 
* V1.1.1 (#15)

* add the pow_exp kernel and tested

* all fixes

* resolve threads plus some modifications

* Fix cuda

* fix for linking cuda

* fix: hicma modifactions

* try fixing Jenkines

* Adding R structure

* fix:add doxygen in Jenkines

* add test file for pow-exp kernel

* test with -fpic

* some modifications for HiCMA

* updates

* try 2 gpu devices

* back to starsh

* a potential fix to doxygen

* roll back

* test Rcpp

* Fix Jenkines

* fix errors

* Updated in design

* updates

* all release issue without src checks

* adding MakeFile

* Updated MPI

* Documentation

* fix examples tests

* modeling takes pointers

* example for read and write data

* fix: typpo in Initialize

* fix passing numbers of theta

* fix: performance of gsl

* fix: GPU support

* fix:mspe

* updated devel

* R branch init

* tests:add r tests

* fix tests

* bug: in tlr

* fix:tlr

* fix Jenkines

* fix: Jenkines in Documentation

* minior updates

* huge refactoring

* full R

* potential for tlr issue

* updates in heavy tests

* a fix for gpu in gaussian kernels

* smalling tlr size

* update sizes of heavy_tests

* smalling size for gpu

* minior changes

* Huge refactoring in docs

* resolve threads

* fix MPI

* resolve thread

* updated R documentation

* documentation and hardware changes

* finalized documentations

* minior change in Hardware

* Ft test mpi mk (#6)

* solve multi thread issue in MPI

* Fix MPI tests with chameleon

* Fixed HiCMA with MPI

* update license

* minior cleanings (#7)

* v1.1.0 (#4) (#8)

* add the pow_exp kernel and tested

* all fixes

* resolve threads plus some modifications

* Fix cuda

* fix for linking cuda

* fix: hicma modifactions

* try fixing Jenkines

* Adding R structure

* fix:add doxygen in Jenkines

* add test file for pow-exp kernel

* test with -fpic

* some modifications for HiCMA

* updates

* try 2 gpu devices

* back to starsh

* a potential fix to doxygen

* roll back

* test Rcpp

* Fix Jenkines

* fix errors

* Updated in design

* updates

* all release issue without src checks

* adding MakeFile

* Updated MPI

* Documentation

* fix examples tests

* modeling takes pointers

* example for read and write data

* fix: typpo in Initialize

* fix passing numbers of theta

* fix: performance of gsl

* fix: GPU support

* fix:mspe

* updated devel

* R branch init

* tests:add r tests

* fix tests

* bug: in tlr

* fix:tlr

* fix Jenkines

* fix: Jenkines in Documentation

* minior updates

* huge refactoring

* full R

* potential for tlr issue

* updates in heavy tests

* a fix for gpu in gaussian kernels

* smalling tlr size

* update sizes of heavy_tests

* smalling size for gpu

* minior changes

* Huge refactoring in docs

* resolve threads

* fix MPI

* resolve thread

* updated R documentation

* documentation and hardware changes

* finalized documentations

* minior change in Hardware

* Ft test mpi mk (#6)

* solve multi thread issue in MPI

* Fix MPI tests with chameleon

* Fixed HiCMA with MPI

* update license

* minior cleanings (#7)

---------

Co-authored-by: Sameh M. Abdulah <abdullsm@kw60194.kaust.edu.sa>
Co-authored-by: Mahmoud Karargy <x_karargma@almaha.kaust.edu.sa>

* Fix P & Q

* updates in R (#9)

* Fix error in R

* Fix using of openblas (#16)

---------

Co-authored-by: Sameh M. Abdulah <abdullsm@kw60194.kaust.edu.sa>
Co-authored-by: Mahmoud Karargy <x_karargma@almaha.kaust.edu.sa>

* V1.1.2 (#17)

* Fixed cmake installation and add  requirements in ReadME

* All fixes for hicma

* Modify README.md (#22)

* modify README.md

* more edits to README.md

* more minor edits

* more minor edits to the R example

* fix the R code

* remove empty line

---------

Co-authored-by: Sameh M. Abdulah <abdullsm@kw60194.kaust.edu.sa>
Co-authored-by: Mahmoud Karargy <x_karargma@almaha.kaust.edu.sa>
Co-authored-by: Sameh Abdulah <23186151+SAbdulah@users.noreply.github.com>
@mahmoudElkarargyBS @SAbdulah
Ft add accuracy tlr (#26)
8c655ab 
* V1.1.1 (#15)

* add the pow_exp kernel and tested

* all fixes

* resolve threads plus some modifications

* Fix cuda

* fix for linking cuda

* fix: hicma modifactions

* try fixing Jenkines

* Adding R structure

* fix:add doxygen in Jenkines

* add test file for pow-exp kernel

* test with -fpic

* some modifications for HiCMA

* updates

* try 2 gpu devices

* back to starsh

* a potential fix to doxygen

* roll back

* test Rcpp

* Fix Jenkines

* fix errors

* Updated in design

* updates

* all release issue without src checks

* adding MakeFile

* Updated MPI

* Documentation

* fix examples tests

* modeling takes pointers

* example for read and write data

* fix: typpo in Initialize

* fix passing numbers of theta

* fix: performance of gsl

* fix: GPU support

* fix:mspe

* updated devel

* R branch init

* tests:add r tests

* fix tests

* bug: in tlr

* fix:tlr

* fix Jenkines

* fix: Jenkines in Documentation

* minior updates

* huge refactoring

* full R

* potential for tlr issue

* updates in heavy tests

* a fix for gpu in gaussian kernels

* smalling tlr size

* update sizes of heavy_tests

* smalling size for gpu

* minior changes

* Huge refactoring in docs

* resolve threads

* fix MPI

* resolve thread

* updated R documentation

* documentation and hardware changes

* finalized documentations

* minior change in Hardware

* Ft test mpi mk (#6)

* solve multi thread issue in MPI

* Fix MPI tests with chameleon

* Fixed HiCMA with MPI

* update license

* minior cleanings (#7)

* v1.1.0 (#4) (#8)

* add the pow_exp kernel and tested

* all fixes

* resolve threads plus some modifications

* Fix cuda

* fix for linking cuda

* fix: hicma modifactions

* try fixing Jenkines

* Adding R structure

* fix:add doxygen in Jenkines

* add test file for pow-exp kernel

* test with -fpic

* some modifications for HiCMA

* updates

* try 2 gpu devices

* back to starsh

* a potential fix to doxygen

* roll back

* test Rcpp

* Fix Jenkines

* fix errors

* Updated in design

* updates

* all release issue without src checks

* adding MakeFile

* Updated MPI

* Documentation

* fix examples tests

* modeling takes pointers

* example for read and write data

* fix: typpo in Initialize

* fix passing numbers of theta

* fix: performance of gsl

* fix: GPU support

* fix:mspe

* updated devel

* R branch init

* tests:add r tests

* fix tests

* bug: in tlr

* fix:tlr

* fix Jenkines

* fix: Jenkines in Documentation

* minior updates

* huge refactoring

* full R

* potential for tlr issue

* updates in heavy tests

* a fix for gpu in gaussian kernels

* smalling tlr size

* update sizes of heavy_tests

* smalling size for gpu

* minior changes

* Huge refactoring in docs

* resolve threads

* fix MPI

* resolve thread

* updated R documentation

* documentation and hardware changes

* finalized documentations

* minior change in Hardware

* Ft test mpi mk (#6)

* solve multi thread issue in MPI

* Fix MPI tests with chameleon

* Fixed HiCMA with MPI

* update license

* minior cleanings (#7)

---------

Co-authored-by: Sameh M. Abdulah <abdullsm@kw60194.kaust.edu.sa>
Co-authored-by: Mahmoud Karargy <x_karargma@almaha.kaust.edu.sa>

* Fix P & Q

* updates in R (#9)

* Fix error in R

* Fix using of openblas (#16)

---------

Co-authored-by: Sameh M. Abdulah <abdullsm@kw60194.kaust.edu.sa>
Co-authored-by: Mahmoud Karargy <x_karargma@almaha.kaust.edu.sa>

* V1.1.2 (#17)

* Fixed cmake installation and add  requirements in ReadME

* All fixes for hicma

* Modify README.md (#22)

* modify README.md

* more edits to README.md

* more minor edits

* more minor edits to the R example

* fix the R code

* remove empty line

* debuging prints

* cleaner version

---------

Co-authored-by: Sameh M. Abdulah <abdullsm@kw60194.kaust.edu.sa>
Co-authored-by: Mahmoud Karargy <x_karargma@almaha.kaust.edu.sa>
Co-authored-by: Sameh Abdulah <23186151+SAbdulah@users.noreply.github.com>
@mahmoudElkarargyBS
change value of acc
e2af57e
@mahmoudElkarargyBS
update params values
97690fe
@SAbdulah
Use random seed by default unless user specifies one (#29)
a25a9d1 
# updated devel branch to match master and also fixed tests
@omar-hmarzouk @mahmoudElkarargyBS
Fix tlr bug fix om (#30)
cb90515 
* TLR Issue resolved -- zgytlr changed to dgytlr and accuracy calculation fixed

* alignment and reformatting

---------

Co-authored-by: mahmoud <mahmoud.elkarargy@brightskiesinc.com>
@alihakam830
added missing header to configurations for gcc v14.1.0 support (#38)
9dc7d01
@mahmoudElkarargyBS
requirment for CUDA <12
1f9ce46
@mahmoudElkarargyBS
resolve conflicts
2cf4a09
@SAbdulah
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The commit is too large. Please try to reduce the size of future commits.

@SAbdulah
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CMake Error at CMakeLists.txt:53 (message): CUDA 13.0.48 detected. This project only supports CUDA < 12. Please install an older CUDA toolkit.

Why is this?

@mahmoudElkarargyBS
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CMake Error at CMakeLists.txt:53 (message): CUDA 13.0.48 detected. This project only supports CUDA < 12. Please install an older CUDA toolkit.

Why is this?

Check reply here: #34

@mahmoudElkarargyBS
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The commit is too large. Please try to reduce the size of future commits.

Kindly check changes, most of the files are regarding the kernels testing, as I need to set the seed with zero after we now have a randomly generated one.

@SAbdulah
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If curl is mandatory, so let's add it to the README file @mahmoudElkarargyBS

@mahmoudElkarargyBS mahmoudElkarargyBS merged commit 4930620 into main Sep 28, 2025
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@mahmoudElkarargyBS @SAbdulah @omar-hmarzouk @alihakam830