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Merge branch 'jgfouca/cime/fixes_for_titan' (PR #1321)
Restore Titan support after CIME5.2 merge. A number of issues prevented successful create, set-up, build and run phases on Titan after the merge of CIME5.2. Even with these resolved, some functionality was lost, e.g. support for using a different number of MPI tasks per node for nonoverlapping components and support for more than one compiler. Finally, support for netcdf4 files was missing when using PGI. 1) Remove CESM_REPO. 2) Add better support for netcdf and pnetcdf in config*.xml . 3) Use findNetcdf.cmake from pio2 in pio1. 4) Use newer cmake, required by pio2. 5) Fix aprun command construction. 6) Fix Macro maker, to enable multiple compiler support. 7) Update modules and paths to enable netcdf4 support and multiple compiler support. Testing has focused on production-like cases, including low resolution water cycle and high resolution GMPAS, both with and without the v3 MPAS meshes and with a number of different PE layouts. acme_developer is not yet working, for reasons distinct from the pull request, and without these changes, progress will not be possible on getting the acme_developer to work again. A unit test was added for the updated aprun command construction capability, and this was passed. * jgfouca/cime/fixes_for_titan: Fix type in melvin config change update modules to support netcdf4 files on Titan Fix macro maker Make netcdfroot less hardcoded for titan Fix spelling of NTHRDS Remove outdated comment Add test for intel compiler Add unit test Re-introduce task_maker algorithm to compute aprun Fixing walltime for titan debug queue Fix aprun command construction Numerous titan fixes.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,133 @@ | ||
| """ | ||
| Aprun is far too complex to handle purely through XML. We need python | ||
| code to compute and assemble aprun commands. | ||
| """ | ||
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| from CIME.XML.standard_module_setup import * | ||
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| import math | ||
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| logger = logging.getLogger(__name__) | ||
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| ############################################################################### | ||
| def _get_aprun_cmd_for_case_impl(ntasks, nthreads, rootpes, pstrids, | ||
| max_tasks_per_node, pes_per_node, | ||
| pio_numtasks, pio_async_interface, | ||
| compiler, machine, run_exe): | ||
| ############################################################################### | ||
| """ | ||
| No one really understands this code, but we can at least test it. | ||
| >>> ntasks = [512, 675, 168, 512, 128, 168, 168, 512, 1] | ||
| >>> nthreads = [2, 2, 2, 2, 4, 2, 2, 2, 1] | ||
| >>> rootpes = [0, 0, 512, 0, 680, 512, 512, 0, 0] | ||
| >>> pstrids = [1, 1, 1, 1, 1, 1, 1, 1, 1] | ||
| >>> max_tasks_per_node = 16 | ||
| >>> pes_per_node = 16 | ||
| >>> pio_numtasks = -1 | ||
| >>> pio_async_interface = False | ||
| >>> compiler = "pgi" | ||
| >>> machine = "titan" | ||
| >>> run_exe = "acme.exe" | ||
| >>> _get_aprun_cmd_for_case_impl(ntasks, nthreads, rootpes, pstrids, max_tasks_per_node, pes_per_node, pio_numtasks, pio_async_interface, compiler, machine, run_exe) | ||
| 'aprun -S 4 -n 680 -N 8 -d 2 acme.exe : -S 2 -n 128 -N 4 -d 4 acme.exe ' | ||
| >>> compiler = "intel" | ||
| >>> _get_aprun_cmd_for_case_impl(ntasks, nthreads, rootpes, pstrids, max_tasks_per_node, pes_per_node, pio_numtasks, pio_async_interface, compiler, machine, run_exe) | ||
| 'aprun -S 4 -cc numa_node -n 680 -N 8 -d 2 acme.exe : -S 2 -cc numa_node -n 128 -N 4 -d 4 acme.exe ' | ||
| """ | ||
| max_tasks_per_node = 1 if max_tasks_per_node < 1 else max_tasks_per_node | ||
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| total_tasks = 0 | ||
| for ntask, rootpe, pstrid in zip(ntasks, rootpes, pstrids): | ||
| tt = rootpe + (ntask - 1) * pstrid + 1 | ||
| total_tasks = max(tt, total_tasks) | ||
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| # Check if we need to add pio's tasks to the total task count | ||
| if pio_async_interface: | ||
| total_tasks += pio_numtasks if pio_numtasks > 0 else pes_per_node | ||
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| # Compute max threads for each mpi task | ||
| maxt = [0] * total_tasks | ||
| for ntask, nthrd, rootpe, pstrid in zip(ntasks, nthreads, rootpes, pstrids): | ||
| c2 = 0 | ||
| while c2 < ntask: | ||
| s = rootpe + c2 * pstrid | ||
| if nthrd > maxt[s]: | ||
| maxt[s] = nthrd | ||
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| c2 += 1 | ||
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| logger.info("total tasks is: %s" % total_tasks) | ||
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| # make sure all maxt values at least 1 | ||
| for c1 in xrange(0, total_tasks): | ||
| if maxt[c1] < 1: | ||
| maxt[c1] = 1 | ||
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| # Compute task and thread settings for batch commands | ||
| tasks_per_node, task_count, thread_count, max_thread_count, aprun = \ | ||
| 0, 1, maxt[0], maxt[0], "aprun" | ||
| for c1 in xrange(1, total_tasks): | ||
| if maxt[c1] != thread_count: | ||
| tasks_per_node = min(pes_per_node, max_tasks_per_node / thread_count) | ||
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| tasks_per_node = min(task_count, tasks_per_node) | ||
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| # Compute for every subset | ||
| task_per_numa = int(math.ceil(tasks_per_node / 2.0)) | ||
| # Option for Titan | ||
| if machine == "titan" and tasks_per_node > 1: | ||
| aprun += " -S %d" % task_per_numa | ||
| if compiler == "intel": | ||
| aprun += " -cc numa_node" | ||
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| aprun += " -n %d -N %d -d %d %s :" % (task_count, tasks_per_node, thread_count, run_exe) | ||
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| thread_count = maxt[c1] | ||
| max_thread_count = max(max_thread_count, maxt[c1]) | ||
| task_count = 1 | ||
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| else: | ||
| task_count += 1 | ||
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| if pes_per_node > 0: | ||
| tasks_per_node = min(pes_per_node, max_tasks_per_node / thread_count) | ||
| else: | ||
| tasks_per_node = max_tasks_per_node / thread_count | ||
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| tasks_per_node = min(task_count, tasks_per_node) | ||
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| task_per_numa = int(math.ceil(tasks_per_node / 2.0)) | ||
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| # Special option for Titan with intel compiler | ||
| if machine == "titan" and tasks_per_node > 1: | ||
| aprun += " -S %d" % task_per_numa | ||
| if compiler == "intel": | ||
| aprun += " -cc numa_node" | ||
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| aprun += " -n %d -N %d -d %d %s " % (task_count, tasks_per_node, thread_count, run_exe) | ||
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| return aprun | ||
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| ############################################################################### | ||
| def get_aprun_cmd_for_case(case, run_exe): | ||
| ############################################################################### | ||
| """ | ||
| Given a case, construct and return the aprun command | ||
| """ | ||
| models = case.get_values("COMP_CLASSES") | ||
| ntasks, nthreads, rootpes, pstrids = [], [], [], [] | ||
| for model in models: | ||
| model = "CPL" if model == "DRV" else model | ||
| for the_list, item_name in zip([ntasks, nthreads, rootpes, pstrids], | ||
| ["NTASKS", "NTHRDS", "ROOTPE", "PSTRID"]): | ||
| the_list.append(case.get_value("_".join([item_name, model]))) | ||
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| return _get_aprun_cmd_for_case_impl(ntasks, nthreads, rootpes, pstrids, | ||
| case.get_value("MAX_TASKS_PER_NODE"), | ||
| case.get_value("PES_PER_NODE"), | ||
| case.get_value("PIO_NUMTASKS"), | ||
| case.get_value("PIO_ASYNC_INTERFACE"), | ||
| case.get_value("COMPILER"), | ||
| case.get_value("MACH"), | ||
| run_exe) |
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