From ef592c060f991079533eddeb4a38c414484922e2 Mon Sep 17 00:00:00 2001 From: Sandra Date: Wed, 30 Sep 2020 17:49:58 +0200 Subject: [PATCH 1/9] Saiph: saiph shell --- garlic/saiph/shell.nix | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 garlic/saiph/shell.nix diff --git a/garlic/saiph/shell.nix b/garlic/saiph/shell.nix new file mode 100644 index 0000000..2033d20 --- /dev/null +++ b/garlic/saiph/shell.nix @@ -0,0 +1,14 @@ +with (import ../../default.nix); +with bsc; + +stdenv.mkDerivation rec { + name = "shell"; + buildInputs = [ + clangOmpss2 + impi + nanos6 + tampi + vtk + boost + ]; +} From e3349bb86483b875c84dc739fab3d37ba314b4af Mon Sep 17 00:00:00 2001 From: Sandra Date: Wed, 30 Sep 2020 17:53:13 +0200 Subject: [PATCH 2/9] saiph: exp: adding extrae config files --- garlic/exp/saiph/extraeOPENMPI_OMP.xml | 83 +++++++++++++++++++ garlic/exp/saiph/extraeOPENMPI_OMPSS.xml | 100 +++++++++++++++++++++++ garlic/exp/saiph/myextrae.xml | 0 3 files changed, 183 insertions(+) create mode 100644 garlic/exp/saiph/extraeOPENMPI_OMP.xml create mode 100644 garlic/exp/saiph/extraeOPENMPI_OMPSS.xml create mode 100644 garlic/exp/saiph/myextrae.xml diff --git a/garlic/exp/saiph/extraeOPENMPI_OMP.xml b/garlic/exp/saiph/extraeOPENMPI_OMP.xml new file mode 100644 index 0000000..0cd470c --- /dev/null +++ b/garlic/exp/saiph/extraeOPENMPI_OMP.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + PAPI_TOT_INS,PAPI_TOT_CYC,PAPI_L1_DCM,PAPI_L2_DCM,PAPI_L3_TCM,PAPI_BR_INS,PAPI_BR_MSP,RESOURCE_STALLS + + + PAPI_TOT_INS,PAPI_TOT_CYC,PAPI_VEC_SP,PAPI_SR_INS,PAPI_LD_INS,PAPI_FP_INS + PAPI_TOT_CYC + + + + + + + + + + + + TRACE + 5 + /scratch + /gpfs/scratch/bsc41/bsc41273 + + + + 5000000 + + + + + /gpfs/scratch/bsc41/bsc41273/control + + + + + 10M + + + + + + + + + + + + + + + diff --git a/garlic/exp/saiph/extraeOPENMPI_OMPSS.xml b/garlic/exp/saiph/extraeOPENMPI_OMPSS.xml new file mode 100644 index 0000000..3349d29 --- /dev/null +++ b/garlic/exp/saiph/extraeOPENMPI_OMPSS.xml @@ -0,0 +1,100 @@ + + + + + + + + + + + + + + + + + 1-3 + 1-5 + 1-3 + 1-3 + 1-3 + + + + + + + + + + PAPI_TOT_INS,PAPI_TOT_CYC,PAPI_L1_DCM,PAPI_L2_DCM,PAPI_L3_TCM,PAPI_BR_INS,PAPI_BR_MSP,RESOURCE_STALLS + + + PAPI_TOT_INS,PAPI_TOT_CYC,PAPI_VEC_SP,PAPI_SR_INS,PAPI_LD_INS,PAPI_FP_INS + PAPI_TOT_CYC + + + + + + + + + + + + TRACE + 5 + /scratch + /gpfs/scratch/bsc41/bsc41273 + + + + 5000000 + + + + + /gpfs/scratch/bsc41/bsc41273/control + + + + + 10M + + + + + + 500u + + + + + + + + + + + + + + diff --git a/garlic/exp/saiph/myextrae.xml b/garlic/exp/saiph/myextrae.xml new file mode 100644 index 0000000..e69de29 From 8f5c5146b37d60c5a230166a2f0c379e82dbcd79 Mon Sep 17 00:00:00 2001 From: Sandra Date: Wed, 30 Sep 2020 18:33:08 +0200 Subject: [PATCH 3/9] Saiph: update branchname according to garlic nomenclature --- garlic/exp/saiph/numcomm.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/garlic/exp/saiph/numcomm.nix b/garlic/exp/saiph/numcomm.nix index 0755147..9c306dc 100644 --- a/garlic/exp/saiph/numcomm.nix +++ b/garlic/exp/saiph/numcomm.nix @@ -18,7 +18,7 @@ let # Common configuration common = { # Compile time nbody config - gitBranch = "Saiph_TAMPI_OMPSS"; + gitBranch = "garlic/tampi+isend+oss+task+simd"; mpi = pkgs.bsc.impi; # Resources From 6a2d865225510a4c56dad2bb7e86a703b05c534d Mon Sep 17 00:00:00 2001 From: Sandra Date: Wed, 30 Sep 2020 18:33:27 +0200 Subject: [PATCH 4/9] saiph: adding ministat app to saiph shell --- garlic/saiph/shell.nix | 1 + 1 file changed, 1 insertion(+) diff --git a/garlic/saiph/shell.nix b/garlic/saiph/shell.nix index 2033d20..24cbb42 100644 --- a/garlic/saiph/shell.nix +++ b/garlic/saiph/shell.nix @@ -10,5 +10,6 @@ stdenv.mkDerivation rec { tampi vtk boost + ministat ]; } From 78b96c1bc6c9b1b64e1fc456f4ccc71d906000d4 Mon Sep 17 00:00:00 2001 From: Sandra Date: Wed, 30 Sep 2020 18:34:14 +0200 Subject: [PATCH 5/9] saiph: including reservation option --- garlic/exp/saiph/numcomm.nix | 25 +++++++++++++++++-------- 1 file changed, 17 insertions(+), 8 deletions(-) diff --git a/garlic/exp/saiph/numcomm.nix b/garlic/exp/saiph/numcomm.nix index 9c306dc..07e108c 100644 --- a/garlic/exp/saiph/numcomm.nix +++ b/garlic/exp/saiph/numcomm.nix @@ -44,14 +44,23 @@ let w = runWrappers; - sbatch = {stage, conf, ...}: with conf; w.sbatch { - program = stageProgram stage; - exclusive = true; - time = "02:00:00"; - qos = "debug"; - jobName = "saiph"; - inherit nixPrefix nodes ntasksPerNode; - }; + sbatch = {stage, conf, ...}: with conf; w.sbatch ( + # Allow a user to define a custom reservation for the job in MareNostrum4, + # by setting the garlic.sbatch.reservation attribute in the + # ~/.config/nixpkgs/config.nix file. If the attribute is not set, no + # reservation is used. The user reservation may be overwritten by the + # experiment, if the reservation is set like with nodes or ntasksPerNode. + optionalAttrs (pkgs.config ? garlic.sbatch.reservation) { + inherit (pkgs.config.garlic.sbatch) reservation; + } // { + program = stageProgram stage; + exclusive = true; + time = "02:00:00"; + qos = "debug"; + jobName = "saiph"; + inherit nixPrefix nodes ntasksPerNode; + } + ); control = {stage, conf, ...}: with conf; w.control { program = stageProgram stage; From ce7566cf7afb7807b286bdf8fd40d3d1095028dd Mon Sep 17 00:00:00 2001 From: Sandra Date: Thu, 1 Oct 2020 17:45:40 +0200 Subject: [PATCH 6/9] saiph: removing useless exports --- garlic/saiph/default.nix | 8 -------- 1 file changed, 8 deletions(-) diff --git a/garlic/saiph/default.nix b/garlic/saiph/default.nix index 91a1c36..3028042 100644 --- a/garlic/saiph/default.nix +++ b/garlic/saiph/default.nix @@ -38,19 +38,11 @@ stdenv.mkDerivation rec { # Required for nanos6 hardeningDisable = [ "bindnow" ]; -# Enable debug -# postPatch = '' -# sed -i 's/^SANITIZE_FLAGS=/SANITIZE_FLAGS=$(DEBUG_FLAGS)/g' \ -# saiphv2/cpp/src/Makefile.clang -# ''; - preBuild = '' cd saiphv2/cpp/src export VTK_VERSION=8.2 export VTK_HOME=${vtk} - export BOOST_HOME=${boost} - export SAIPH_HOME=. ''; makeFlags = [ From dcf64bd1f6eaedd6b20e3d5e00c0775089e55afa Mon Sep 17 00:00:00 2001 From: Sandra Date: Thu, 1 Oct 2020 17:49:27 +0200 Subject: [PATCH 7/9] adding NOISE point --- NOISE | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/NOISE b/NOISE index 2f4ded6..cab9f35 100644 --- a/NOISE +++ b/NOISE @@ -99,5 +99,12 @@ ABSTRACT In bscpkgs the symbolic links have been removed for the clangOmpss2 compiler. +1.7 Nix-shell does not allow isolation + + Nix-shell is not isolated, the compilation process tries then to + use headers and libs from /usr. + + This can induce compilation errors not happening inside nix-build. + Do not use to ensure reproducibility. /* vim: set ts=2 sw=2 tw=72 fo=watqc expandtab spell autoindent: */ From cec7a280c02ba606783cb5686cbdad79d9a2b251 Mon Sep 17 00:00:00 2001 From: Sandra Date: Thu, 1 Oct 2020 17:50:07 +0200 Subject: [PATCH 8/9] saiph: removing nix-shell to avoid its use!! --- garlic/saiph/shell.nix | 15 --------------- 1 file changed, 15 deletions(-) delete mode 100644 garlic/saiph/shell.nix diff --git a/garlic/saiph/shell.nix b/garlic/saiph/shell.nix deleted file mode 100644 index 24cbb42..0000000 --- a/garlic/saiph/shell.nix +++ /dev/null @@ -1,15 +0,0 @@ -with (import ../../default.nix); -with bsc; - -stdenv.mkDerivation rec { - name = "shell"; - buildInputs = [ - clangOmpss2 - impi - nanos6 - tampi - vtk - boost - ministat - ]; -} From 79a4a4d16b671a1d40ec4af4a009ec4ff18507ad Mon Sep 17 00:00:00 2001 From: Sandra Date: Fri, 2 Oct 2020 10:46:56 +0200 Subject: [PATCH 9/9] saiph: removing home paths --- garlic/exp/saiph/extraeOPENMPI_OMP.xml | 1 - garlic/exp/saiph/extraeOPENMPI_OMPSS.xml | 1 - 2 files changed, 2 deletions(-) diff --git a/garlic/exp/saiph/extraeOPENMPI_OMP.xml b/garlic/exp/saiph/extraeOPENMPI_OMP.xml index 0cd470c..a8e46e3 100644 --- a/garlic/exp/saiph/extraeOPENMPI_OMP.xml +++ b/garlic/exp/saiph/extraeOPENMPI_OMP.xml @@ -1,7 +1,6 @@ diff --git a/garlic/exp/saiph/extraeOPENMPI_OMPSS.xml b/garlic/exp/saiph/extraeOPENMPI_OMPSS.xml index 3349d29..7cd2fdc 100644 --- a/garlic/exp/saiph/extraeOPENMPI_OMPSS.xml +++ b/garlic/exp/saiph/extraeOPENMPI_OMPSS.xml @@ -1,7 +1,6 @@