A new fat node has been added to the cluster. This is based on an Intel Core i7-13700KF (1700/3.4 GHz/30 MB), an NVIDIA MSI RTX 4070 Ti VENTUS 3X 12Gb OC 3, 8GB DDR4@3200 MHz, and two 2TB disks in a RAID1 array.

Initial tests confirmed that this is our new fastest machine, delivering with gromacs and HMR ~3930 ns/day on the FipWW 8,000 atom/5fs system. As with the other machines, with smaller systems the performance flattens at approximately ~4.1 μs/day (again with gromacs & HMR).

New node added to the cluster

A new fat node has been added to the cluster. This is based on an Intel i9-9900K, an RTX2070S, 8GB DDR4@3000 MHz, and a 2TB disk.

Initial tests confirmed that this is our new fastest machine, delivering ~575 ns/day on the standard 10,000 atom/4fs benchmark. As with the other i9, with smaller systems the performance flattens at approximately ~700ns/day with a 2.5fs step.

New fat box arrived

A new fat node has been added to the cluster. This is based on an Intel i9-9900K, a GTX-1080, 8GB DDR4@3000 MHz, and a two-disk RAID 0 @ 4TB.

Initial tests confirmed that this is indeed our new fastest machine, delivering ~560 ns/day on the standard 10,000 atom benchmark (second best is this one with 460 ns/day). With smaller systems, however, the performance flattens (giving with the CLN025 system 570 ns/day@2fs, ~730 ns/day@2.5fs).

New fat compute node arrived

New fat compute node arrived. It contains an i7-6800K@3.4GHz, an nvidia GTX-1070, 16 GBytes of physical memory and two WD Red 1TB disks. After a few problems with setting-up the disks as RAID0 (using Intel's rapid storage), a minimal CentOS 7.3 was installed and the nvidia drivers compiled and installed.

First tests with NAMD 2.12 were impressive : on a small peptide problem with 4400 atoms, the new box delivered ~330 nanoseconds per day, a speed-up by a factor of 10 compared with NAMD 2.9 running on a node containing an 8-core AMD FX-8150 plus a GTX 570. To make the comparison hardware-dependent-only, we should test with NAMD 2.9 on the new box (testing new NAMD on the old box won't do because support for fermi GPUs was dropped with NAMD 2.12).

On the same peptide system (4300 atoms) and with a 2.5 fs time step, 470 ns/day were recorded. This reached an outstanding 550 ns/day for a smaller (3300 atoms) system. Think about it again : more than 1 μs in two days. Two days.

Update : It seems that with this hardware and NAMD 2.12 it is necessary to disable off-loading FFT to the GPU by using the 'usePMECUDA no' configuration option.

New machine for cluster

New box with an 8-core AMD FX-8150, an NVIDIA GTX 570 and 4 Gbytes of memory at 1333 MHz arrived. After a few problems with perceus (rejected hardware address starting from 8C:…), all else appear to have worked smoothly. Started testing it with NAMD ... [results]

New GPU : Gigabyte's GTX 460

New nvidia GTX 460 installed on cluster. This is the gigabyte version of the card with a double fan. Very nice :