Merge pull request #67 from hpc-io/update-sample-mode

This closes #65
hpc-io · Oct 4, 2022 · ec75a46 · ec75a46
2 parents e162afb + 9d2c2ab
commit ec75a46
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Showing 11 changed files with 27 additions and 19 deletions.
diff --git a/.github/workflows/h5bench-hdf5-develop-test.yml b/.github/workflows/h5bench-hdf5-develop-test.yml
@@ -12,6 +12,7 @@ jobs:
     env:
       OMPI_ALLOW_RUN_AS_ROOT: 1
       OMPI_ALLOW_RUN_AS_ROOT_CONFIRM: 1
+      OMPI_MCA_rmaps_base_oversubscribe: "yes"
 
     steps:
       - uses: actions/checkout@v2
@@ -21,7 +22,7 @@ jobs:
       - name: Dependencies
         run: |
           sudo apt-get update
-          sudo apt-get install cmake gcc libtool zlib1g-dev python3 libopenmpi-dev -y
+          sudo apt-get install cmake gcc gdb libtool zlib1g-dev python3 libopenmpi-dev -y
           
           # HDF5
           git clone https://github.com/HDFGroup/hdf5.git
@@ -167,4 +168,4 @@ jobs:
         with:
           name: test
           path: build*/storage/**/std*
-          retention-days: 1
+          retention-days: 1
diff --git a/.github/workflows/h5bench-hdf5-develop.yml b/.github/workflows/h5bench-hdf5-develop.yml
@@ -12,6 +12,7 @@ jobs:
     env:
       OMPI_ALLOW_RUN_AS_ROOT: 1
       OMPI_ALLOW_RUN_AS_ROOT_CONFIRM: 1
+      OMPI_MCA_rmaps_base_oversubscribe: "yes"
 
     steps:
       - uses: actions/checkout@v2
@@ -21,7 +22,7 @@ jobs:
       - name: Dependencies
         run: |
           sudo apt-get update
-          sudo apt-get install cmake gcc libtool zlib1g-dev python3 libopenmpi-dev -y
+          sudo apt-get install cmake gcc gdb libtool zlib1g-dev python3 libopenmpi-dev -y
           
           # HDF5
           git clone https://github.com/HDFGroup/hdf5.git
@@ -152,6 +153,10 @@ jobs:
 
           cd build-sync
           ./h5bench --debug --abort-on-failure --validate-mode ../samples/sync-write-read-contig-1d-small.json
+        
+      - name: Setup tmate session
+        if: ${{ failure() }}
+        uses: mxschmitt/action-tmate@v3
 
       - name: Test h5bench SYNC write 1D contiguous (memory) strided (file)
         run: |
@@ -641,4 +646,4 @@ jobs:
         with:
           name: test
           path: build*/storage/**/std*
-          retention-days: 1
+          retention-days: 1
diff --git a/commons/h5bench_util.c b/commons/h5bench_util.c
@@ -67,13 +67,13 @@ h5bench_sleep(duration sleep_time)
 }
 
 void
-async_sleep(hid_t file_id, hid_t fapl, duration sleep_time)
+async_sleep(hid_t es_id, duration sleep_time)
 {
 #ifdef USE_ASYNC_VOL
-    unsigned cap = 0;
-    H5Pget_vol_cap_flags(fapl, &cap);
-    if (H5VL_CAP_FLAG_ASYNC & cap)
-        H5Fstart(file_id, fapl);
+    size_t  num_in_progress;
+    hbool_t op_failed;
+
+    H5ESwait(es_id, 0, &num_in_progress, &op_failed);
 #endif
     h5bench_sleep(sleep_time);
 }

diff --git a/commons/h5bench_util.h b/commons/h5bench_util.h
@@ -168,7 +168,7 @@ typedef struct mem_monitor {
 unsigned long long read_time_val(duration time, time_unit unit);
 
 void h5bench_sleep(duration sleep_time);
-void async_sleep(hid_t file_id, hid_t fapl, duration sleep_time);
+void async_sleep(hid_t es_id, duration sleep_time);
 
 void timestep_es_id_close(time_step *ts, async_mode mode);
 

diff --git a/configuration.json b/configuration.json
@@ -45,7 +45,7 @@
                 "DIM_1": "16777216",
                 "DIM_2": "1",
                 "DIM_3": "1",
-                "ASYNC_MODE": "NON",
+                "MODE": "SYNC",
                 "CSV_FILE": "output.csv"
             }
         },
@@ -115,7 +115,7 @@
                 "DIM_1": "16777216",
                 "DIM_2": "1",
                 "DIM_3": "1",
-                "ASYNC_MODE": "NON",
+                "MODE": "SYNC",
                 "CSV_FILE": "output.csv"
             }
         },
@@ -135,7 +135,7 @@
                 "DIM_1": "16777216",
                 "DIM_2": "1",
                 "DIM_3": "1",
-                "ASYNC_MODE": "NON",
+                "MODE": "SYNC",
                 "CSV_FILE": "output.csv"
             }
         },

diff --git a/docs/source/amrex.rst b/docs/source/amrex.rst
@@ -47,7 +47,8 @@ To run an instance of AMReX HDF5 benchmark you need to include the following in
             "nparticlefile": "2",
             "sleeptime": "2",
             "restart_check": "1",
-            "hdf5compression": "ZFP_ACCURACY#0.001"
+            "hdf5compression": "ZFP_ACCURACY#0.001",
+            "mode": "SYNC"
         }
     }
 
@@ -69,6 +70,7 @@ To read grids from file you need to set: ``grids_from_file``, ``nlevels``, and `
             "sleeptime": "2",
             "restart_check": "1",
             "hdf5compression": "ZFP_ACCURACY#0.001",
+            "mode": "SYNC",
             "nlevs": "3",
             "grids_from_file": "1",
             "ref_ratio_file": "4 2"

diff --git a/h5bench_patterns/h5bench_append.c b/h5bench_patterns/h5bench_append.c
@@ -465,7 +465,7 @@ _run_benchmark_modify(hid_t file_id, hid_t fapl, hid_t gapl, hid_t filespace, be
             if (params.compute_time.time_num >= 0) {
                 if (MY_RANK == 0)
                     printf("Computing... \n");
-                async_sleep(file_id, fapl, params.compute_time);
+                async_sleep(ts->es_meta_close, params.compute_time);
             }
         }
 

diff --git a/h5bench_patterns/h5bench_overwrite.c b/h5bench_patterns/h5bench_overwrite.c
@@ -441,7 +441,7 @@ _run_benchmark_modify(hid_t file_id, hid_t fapl, hid_t gapl, hid_t filespace, be
             if (params.compute_time.time_num >= 0) {
                 if (MY_RANK == 0)
                     printf("Computing... \n");
-                async_sleep(file_id, fapl, params.compute_time);
+                async_sleep(ts->es_meta_close, params.compute_time);
             }
         }
 

diff --git a/h5bench_patterns/h5bench_read.c b/h5bench_patterns/h5bench_read.c
@@ -346,7 +346,7 @@ _run_benchmark_read(hid_t file_id, hid_t fapl, hid_t gapl, hid_t filespace, benc
             if (params.compute_time.time_num >= 0) {
                 if (MY_RANK == 0)
                     printf("Computing... \n");
-                async_sleep(file_id, fapl, params.compute_time);
+                async_sleep(ts->es_meta_close, params.compute_time);
             }
         }
 

diff --git a/h5bench_patterns/h5bench_write.c b/h5bench_patterns/h5bench_write.c
@@ -838,7 +838,7 @@ _run_benchmark_write(bench_params params, hid_t file_id, hid_t fapl, hid_t files
             if (params.compute_time.time_num >= 0) {
                 if (MY_RANK == 0)
                     printf("Computing...\n");
-                async_sleep(file_id, fapl, params.compute_time);
+                async_sleep(ts->es_meta_close, params.compute_time);
             }
         }
 

diff --git a/h5bench_patterns/h5bench_write_unlimited.c b/h5bench_patterns/h5bench_write_unlimited.c
@@ -808,7 +808,7 @@ _run_benchmark_write(bench_params params, hid_t file_id, hid_t fapl, hid_t files
             if (params.compute_time.time_num >= 0) {
                 if (MY_RANK == 0)
                     printf("Computing... \n");
-                async_sleep(file_id, fapl, params.compute_time);
+                async_sleep(ts->es_meta_close, params.compute_time);
             }
         }