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doku:memory [2014/07/30 10:43] – ir | doku:memory [2017/09/01 12:56] – removed ir | ||
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- | ====== Memory intensive Jobs ====== | ||
- | Jobs requiring more than 2 GB per process have several alternatives. They might use | ||
- | - a node with more memory, | ||
- | - a parallel environment with fewer processes | ||
- | - increased virtual memory, or | ||
- | - swap space (still experimental). | ||
- | |||
- | ==== ad 1. node with more memory ==== | ||
- | |||
- | The free space on the nodes of a job can be listed, e.g. by | ||
- | qstat -F mem_free|grep -B 2 < | ||
- | | ||
- | == 256 GB per node == | ||
- | |||
- | there are 2 nodes with 64 cores and 256 GB of memory each which are accessible via the '' | ||
- | < | ||
- | #$ -q highmem.q | ||
- | </ | ||
- | | ||
- | == 64 GB and 128 GB per node == | ||
- | |||
- | several nodes on the VSC-2 have 64 GB or more instead of the 32 GB of the standard nodes. | ||
- | To use one of these nodes, just add ''' | ||
- | |||
- | See also [[doku: | ||
- | |||
- | ==== ad 2. parallel environment with fewer processes | ||
- | |||
- | Jobs using more than 2 GB per process can be executed in one of the parallel environments | ||
- | * mpich8: 4 GB per core | ||
- | * mpich4: 8 GB per core | ||
- | * mpich2: 16 GB per core | ||
- | * mpich1: 32 GB per core | ||
- | |||
- | ---- | ||
- | * mpich: 2 GB or 1 cores per process | ||
- | * mpich8: 4 GB or 2 cores per process | ||
- | * mpich4: 8 GB or 4 cores per process | ||
- | * mpich2: 16 GB or 8 cores per process | ||
- | * mpich1: 32 GB or 16 cores per process | ||
- | |||
- | ---- | ||
- | |||
- | Please keep in mind that on VSC-2 jobs are node-exclusive and therefore your contingent of CPU-hours will be computed by full nodes and are therefore significantly more expensive. | ||
- | For example, < | ||
- | |||
- | |||
- | ---- | ||
- | |||
- | |||
- | The variable NSLOTS_REDUCED is set to the number of cores requested, whereas the variable NSLOTS is set to the number of cores allocated in the queueing system, which corresponds to the cost calculation of the previous paragraph. | ||
- | Replace your calls to mpirun accordingly to< | ||
- | |||
- | |||
- | ---- | ||
- | == jobscript == | ||
- | |||
- | Then parallel environment option (pe) includes the type of the requested environment (mpich2) and the number of processes (4) | ||
- | < | ||
- | export OMP_NUM_THREADS=8 | ||
- | mpirun -machinefile $TMPDIR/ | ||
- | Within the machine file the variable NSLOTS_REDUCED is automatically set to the number of processes/ | ||
- | ==== ad 3. increased virtual memory ==== | ||
- | |||
- | Some programs allocate more memory than they use. This was especially true in old FORTRAN 77 programs, which had to decide at compile time how much memory will be used. These programs are allowed to allocate 50% more memory than available by '''# | ||
- | |||
- | ==== ad 4. swap space (still experimental) ==== | ||
- | |||
- | A novel feature of the VSC-2 is remote swap space (implemented using 'SCSI RDMA Protocol', |