Adding globbing and wordsplitting prevention. #1016

keldu · 2022-04-11T08:32:26Z

Just set some quotes around some variables even though most wouldn't provide attack surfaces.
Defense in depth still is a good concept to follow.

upsj

LGTM!

.github/rebase.sh

.github/format.sh

yhmtsai

LGTM although I think git always generates no-space branch, which replaces space by - when creating branch

tcojean

LGTM.

Did you try the scripts in dev_tools/scripts? I'm sure there we might have more issues.

Also, maybe we should add a shellkcheck job for the few bash scripts we have? See https://github.com/ginkgo-project/gitlab-hpc-ci-cb/blob/master/.github/workflows/shell_check.yml

keldu · 2022-04-19T08:42:58Z

LGTM.

Did you try the scripts in dev_tools/scripts? I'm sure there we might have more issues.

I didn't.
Currently checking it out.

For the start it's a lot of echo | sed calls which shellcheck complains about and suggests using ${variable//search/replace}. Though I am bit unfamiliar with sed syntax. I'll check it out and see if I can reproduce functionality. I think it's a bit too risky though to change these kind of calls.

Also some ${cat file | sed} could be replaced by ${sed ... < file}. That's easier to do.

Will rework that folder today.

Also, maybe we should add a shellkcheck job for the few bash scripts we have? See https://github.com/ginkgo-project/gitlab-hpc-ci-cb/blob/master/.github/workflows/shell_check.yml

I'm not sure what the implications would be, because there are some things which I wouldn't be comfortable to replace.
Mostly because those are styling/clean bash hints.

If shellcheck can provide this level of detail then it should be possible. The checking job shouldn't fail because of echo | sed instead of the bash replace syntax.

tcojean · 2022-04-19T08:52:34Z

I'm not sure what the implications would be, because there are some things which I wouldn't be comfortable to replace. Mostly because those are styling/clean bash hints.

If shellcheck can provide this level of detail then it should be possible. The checking job shouldn't fail because of echo | sed instead of the bash replace syntax.

You can tell shellcheck to ignore some things, like this:
https://github.com/ginkgo-project/gitlab-hpc-ci-cb/blob/master/run.sh#L35-L36

In general though, it does look attractive to not rely on sed, since it's not entirely portable.

codecov · 2022-04-19T17:14:30Z

Codecov Report

Merging #1016 (e394004) into develop (6b59096) will increase coverage by 0.00%.
The diff coverage is n/a.

@@           Coverage Diff            @@
##           develop    #1016   +/-   ##
========================================
  Coverage    91.70%   91.71%           
========================================
  Files          496      496           
  Lines        42408    42407    -1     
========================================
  Hits         38892    38892           
+ Misses        3516     3515    -1

Impacted Files	Coverage Δ
omp/reorder/rcm_kernels.cpp	`98.13% <0.00%> (+0.60%)`	⬆️

Continue to review full report at Codecov.

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stale

yhmtsai

I think bash can not distinguish the nested quote
"AAA"BB"CC" -> ("AAA")(BB)("CCC") not ("AAA(BB)CC")

.github/rebase.sh

dev_tools/oneapi/convert_source.sh

dev_tools/scripts/create_new_algorithm.sh

dev_tools/scripts/cuda2hip.sh

dev_tools/scripts/format_header.sh

dev_tools/scripts/update_ginkgo_header.sh

yhmtsai · 2022-05-03T08:42:55Z

Sorry for confusion. " works when there is ().
if "AAA$(BB"CCC")", it should work as expected. () helps separation

keldu · 2022-05-03T12:14:46Z

Sorry for confusion. " works when there is (). if "AAA$(BB"CCC")", it should work as expected. () helps separation

To be honest, I also didn't know that it would work before I changed the scripts here.
It's a bit confusing, but shellcheck complains if you don't do it.

Bash can handle this

upsj

LGTM! Mostly nits

dev_tools/scripts/create_new_algorithm.sh

keldu · 2022-05-03T12:51:15Z

Rebased and force pushed because of a useless merge

tcojean

LGTM. Some minor issues

dev_tools/oneapi/convert_source.sh

dev_tools/scripts/add_license.sh

dev_tools/scripts/update_ginkgo_header.sh

tcojean · 2022-05-09T08:17:45Z

Random question since it's maybe a good time, do you need to update your mail in the contributors.txt ?

some errors need to be fixed

tcojean

Some changes are required to get back the functionality of create_new_algorithm.sh script.

dev_tools/scripts/create_new_algorithm.sh

…heck and is regarded as an error

Co-authored-by: Tobias Ribizel <ribizel@kit.edu>

Co-authored-by: Yuhsiang M. Tsai <19565938+yhmtsai@users.noreply.github.com>

Co-authored-by: Tobias Ribizel <ribizel@kit.edu>

Co-authored-by: Terry Cojean <terry.cojean@kit.edu>

sonarqubecloud · 2022-07-14T16:30:53Z

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tcojean

LGTM but needs one extra change

tcojean · 2022-07-18T08:40:42Z

dev_tools/scripts/create_new_algorithm.sh

-        for i in $(ls $GINKGO_ROOT_DIR/core/$type/*.cpp)
+        for i in "${GINKGO_ROOT_DIR}/core/${type}/"*.cpp;


This one also needs the ls form

thoasm

LGTM!

Advertise release 1.5.0 and last changes + Add changelog, + Update third party libraries + A small fix to a CMake file See PR: #1195 The Ginkgo team is proud to announce the new Ginkgo minor release 1.5.0. This release brings many important new features such as: - MPI-based multi-node support for all matrix formats and most solvers; - full DPC++/SYCL support, - functionality and interface for GPU-resident sparse direct solvers, - an interface for wrapping solvers with scaling and reordering applied, - a new algebraic Multigrid solver/preconditioner, - improved mixed-precision support, - support for device matrix assembly, and much more. If you face an issue, please first check our [known issues page](https://github.com/ginkgo-project/ginkgo/wiki/Known-Issues) and the [open issues list](https://github.com/ginkgo-project/ginkgo/issues) and if you do not find a solution, feel free to [open a new issue](https://github.com/ginkgo-project/ginkgo/issues/new/choose) or ask a question using the [github discussions](https://github.com/ginkgo-project/ginkgo/discussions). Supported systems and requirements: + For all platforms, CMake 3.13+ + C++14 compliant compiler + Linux and macOS + GCC: 5.5+ + clang: 3.9+ + Intel compiler: 2018+ + Apple LLVM: 8.0+ + NVHPC: 22.7+ + Cray Compiler: 14.0.1+ + CUDA module: CUDA 9.2+ or NVHPC 22.7+ + HIP module: ROCm 4.0+ + DPC++ module: Intel OneAPI 2021.3 with oneMKL and oneDPL. Set the CXX compiler to `dpcpp`. + Windows + MinGW and Cygwin: GCC 5.5+ + Microsoft Visual Studio: VS 2019 + CUDA module: CUDA 9.2+, Microsoft Visual Studio + OpenMP module: MinGW or Cygwin. Algorithm and important feature additions: + Add MPI-based multi-node for all matrix formats and solvers (except GMRES and IDR). ([#676](#676), [#908](#908), [#909](#909), [#932](#932), [#951](#951), [#961](#961), [#971](#971), [#976](#976), [#985](#985), [#1007](#1007), [#1030](#1030), [#1054](#1054), [#1100](#1100), [#1148](#1148)) + Porting the remaining algorithms (preconditioners like ISAI, Jacobi, Multigrid, ParILU(T) and ParIC(T)) to DPC++/SYCL, update to SYCL 2020, and improve support and performance ([#896](#896), [#924](#924), [#928](#928), [#929](#929), [#933](#933), [#943](#943), [#960](#960), [#1057](#1057), [#1110](#1110), [#1142](#1142)) + Add a Sparse Direct interface supporting GPU-resident numerical LU factorization, symbolic Cholesky factorization, improved triangular solvers, and more ([#957](#957), [#1058](#1058), [#1072](#1072), [#1082](#1082)) + Add a ScaleReordered interface that can wrap solvers and automatically apply reorderings and scalings ([#1059](#1059)) + Add a Multigrid solver and improve the aggregation based PGM coarsening scheme ([#542](#542), [#913](#913), [#980](#980), [#982](#982), [#986](#986)) + Add infrastructure for unified, lambda-based, backend agnostic, kernels and utilize it for some simple kernels ([#833](#833), [#910](#910), [#926](#926)) + Merge different CUDA, HIP, DPC++ and OpenMP tests under a common interface ([#904](#904), [#973](#973), [#1044](#1044), [#1117](#1117)) + Add a device_matrix_data type for device-side matrix assembly ([#886](#886), [#963](#963), [#965](#965)) + Add support for mixed real/complex BLAS operations ([#864](#864)) + Add a FFT LinOp for all but DPC++/SYCL ([#701](#701)) + Add FBCSR support for NVIDIA and AMD GPUs and CPUs with OpenMP ([#775](#775)) + Add CSR scaling ([#848](#848)) + Add array::const_view and equivalent to create constant matrices from non-const data ([#890](#890)) + Add a RowGatherer LinOp supporting mixed precision to gather dense matrix rows ([#901](#901)) + Add mixed precision SparsityCsr SpMV support ([#970](#970)) + Allow creating CSR submatrix including from (possibly discontinuous) index sets ([#885](#885), [#964](#964)) + Add a scaled identity addition (M <- aI + bM) feature interface and impls for Csr and Dense ([#942](#942)) Deprecations and important changes: + Deprecate AmgxPgm in favor of the new Pgm name. ([#1149](#1149)). + Deprecate specialized residual norm classes in favor of a common `ResidualNorm` class ([#1101](#1101)) + Deprecate CamelCase non-polymorphic types in favor of snake_case versions (like array, machine_topology, uninitialized_array, index_set) ([#1031](#1031), [#1052](#1052)) + Bug fix: restrict gko::share to rvalue references (*possible interface break*) ([#1020](#1020)) + Bug fix: when using cuSPARSE's triangular solvers, specifying the factory parameter `num_rhs` is now required when solving for more than one right-hand side, otherwise an exception is thrown ([#1184](#1184)). + Drop official support for old CUDA < 9.2 ([#887](#887)) Improved performance additions: + Reuse tmp storage in reductions in solvers and add a mutable workspace to all solvers ([#1013](#1013), [#1028](#1028)) + Add HIP unsafe atomic option for AMD ([#1091](#1091)) + Prefer vendor implementations for Dense dot, conj_dot and norm2 when available ([#967](#967)). + Tuned OpenMP SellP, COO, and ELL SpMV kernels for a small number of RHS ([#809](#809)) Fixes: + Fix various compilation warnings ([#1076](#1076), [#1183](#1183), [#1189](#1189)) + Fix issues with hwloc-related tests ([#1074](#1074)) + Fix include headers for GCC 12 ([#1071](#1071)) + Fix for simple-solver-logging example ([#1066](#1066)) + Fix for potential memory leak in Logger ([#1056](#1056)) + Fix logging of mixin classes ([#1037](#1037)) + Improve value semantics for LinOp types, like moved-from state in cross-executor copy/clones ([#753](#753)) + Fix some matrix SpMV and conversion corner cases ([#905](#905), [#978](#978)) + Fix uninitialized data ([#958](#958)) + Fix CUDA version requirement for cusparseSpSM ([#953](#953)) + Fix several issues within bash-script ([#1016](#1016)) + Fixes for `NVHPC` compiler support ([#1194](#1194)) Other additions: + Simplify and properly name GMRES kernels ([#861](#861)) + Improve pkg-config support for non-CMake libraries ([#923](#923), [#1109](#1109)) + Improve gdb pretty printer ([#987](#987), [#1114](#1114)) + Add a logger highlighting inefficient allocation and copy patterns ([#1035](#1035)) + Improved and optimized test random matrix generation ([#954](#954), [#1032](#1032)) + Better CSR strategy defaults ([#969](#969)) + Add `move_from` to `PolymorphicObject` ([#997](#997)) + Remove unnecessary device_guard usage ([#956](#956)) + Improvements to the generic accessor for mixed-precision ([#727](#727)) + Add a naive lower triangular solver implementation for CUDA ([#764](#764)) + Add support for int64 indices from CUDA 11 onward with SpMV and SpGEMM ([#897](#897)) + Add a L1 norm implementation ([#900](#900)) + Add reduce_add for arrays ([#831](#831)) + Add utility to simplify Dense View creation from an existing Dense vector ([#1136](#1136)). + Add a custom transpose implementation for Fbcsr and Csr transpose for unsupported vendor types ([#1123](#1123)) + Make IDR random initilization deterministic ([#1116](#1116)) + Move the algorithm choice for triangular solvers from Csr::strategy_type to a factory parameter ([#1088](#1088)) + Update CUDA archCoresPerSM ([#1175](#1116)) + Add kernels for Csr sparsity pattern lookup ([#994](#994)) + Differentiate between structural and numerical zeros in Ell/Sellp ([#1027](#1027)) + Add a binary IO format for matrix data ([#984](#984)) + Add a tuple zip_iterator implementation ([#966](#966)) + Simplify kernel stubs and declarations ([#888](#888)) + Simplify GKO_REGISTER_OPERATION with lambdas ([#859](#859)) + Simplify copy to device in tests and examples ([#863](#863)) + More verbose output to array assertions ([#858](#858)) + Allow parallel compilation for Jacobi kernels ([#871](#871)) + Change clang-format pointer alignment to left ([#872](#872)) + Various improvements and fixes to the benchmarking framework ([#750](#750), [#759](#759), [#870](#870), [#911](#911), [#1033](#1033), [#1137](#1137)) + Various documentation improvements ([#892](#892), [#921](#921), [#950](#950), [#977](#977), [#1021](#1021), [#1068](#1068), [#1069](#1069), [#1080](#1080), [#1081](#1081), [#1108](#1108), [#1153](#1153), [#1154](#1154)) + Various CI improvements ([#868](#868), [#874](#874), [#884](#884), [#889](#889), [#899](#899), [#903](#903), [#922](#922), [#925](#925), [#930](#930), [#936](#936), [#937](#937), [#958](#958), [#882](#882), [#1011](#1011), [#1015](#1015), [#989](#989), [#1039](#1039), [#1042](#1042), [#1067](#1067), [#1073](#1073), [#1075](#1075), [#1083](#1083), [#1084](#1084), [#1085](#1085), [#1139](#1139), [#1178](#1178), [#1187](#1187))

upsj assigned keldu Apr 11, 2022

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keldu and others added 22 commits July 14, 2022 09:42

changed from $? to regular bash syntax

fea5b9f

mostly warnings. for in ls is apparently unstable according to shellc…

4fcdd55

…heck and is regarded as an error

Update .github/format.sh

e55f33a

Co-authored-by: Tobias Ribizel <ribizel@kit.edu>

simple word splitting globbing changes

43f48bb

Mostly ! -z to -n changes. Also double quoting

41c6827

Added double quotes

cc9a6eb

Update .github/rebase.sh

5d56673

Co-authored-by: Tobias Ribizel <ribizel@kit.edu>

Update dev_tools/oneapi/convert_source.sh

d46ba37

Co-authored-by: Yuhsiang M. Tsai <19565938+yhmtsai@users.noreply.github.com>

Update dev_tools/scripts/create_new_algorithm.sh

82fff96

Co-authored-by: Yuhsiang M. Tsai <19565938+yhmtsai@users.noreply.github.com>

Update dev_tools/scripts/cuda2hip.sh

3f39777

Co-authored-by: Yuhsiang M. Tsai <19565938+yhmtsai@users.noreply.github.com>

missed quote in dev_tools

b019df8

Update dev_tools/scripts/create_new_algorithm.sh

715c91d

Co-authored-by: Yuhsiang M. Tsai <19565938+yhmtsai@users.noreply.github.com>

move " around todo

71d07a8

Update dev_tools/scripts/create_new_algorithm.sh

ef09a7c

Co-authored-by: Tobias Ribizel <ribizel@kit.edu>

moved " to back

903bb3d

retab

15392ef

Update dev_tools/scripts/create_new_algorithm.sh

cdb255b

Co-authored-by: Terry Cojean <terry.cojean@kit.edu>

Update dev_tools/scripts/create_new_algorithm.sh

0745711

Co-authored-by: Terry Cojean <terry.cojean@kit.edu>

Update dev_tools/oneapi/convert_source.sh

a3c47b8

Co-authored-by: Terry Cojean <terry.cojean@kit.edu>

Update dev_tools/scripts/update_ginkgo_header.sh

cad8c26

Co-authored-by: Terry Cojean <terry.cojean@kit.edu>

Update dev_tools/scripts/add_license.sh

4e85937

Co-authored-by: Terry Cojean <terry.cojean@kit.edu>

revert to ls. not nice, but for now necessary

ef18496

keldu force-pushed the shellchecked branch from da5fe13 to ef18496 Compare July 14, 2022 07:42

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keldu merged commit 396c6c0 into develop Aug 4, 2022

keldu deleted the shellchecked branch August 4, 2022 09:21

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Adding globbing and wordsplitting prevention. #1016

Adding globbing and wordsplitting prevention. #1016

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		for i in $(ls $GINKGO_ROOT_DIR/core/$type/*.cpp)
		for i in "${GINKGO_ROOT_DIR}/core/${type}/"*.cpp;

Adding globbing and wordsplitting prevention. #1016

Adding globbing and wordsplitting prevention. #1016

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