Re: CUDA error cudaMalloc during running namd

From: Vermaas, Josh (
Date: Thu Aug 25 2022 - 11:13:54 CDT

The error message you are getting is because CUDA can’t allocate memory on the GPUs. How big is the system you are trying to simulate? The K620 at this point are downright ancient, and might exceed the 2x2GB that your pair of 620s would have.


From: <> on behalf of SHIVAM TIWARI <>
Reply-To: "" <>, SHIVAM TIWARI <>
Date: Thursday, August 25, 2022 at 7:46 AM
To: namd-l <>
Subject: namd-l: CUDA error cudaMalloc during running namd

Dear all,

I am using a workstation with ubuntu 20.04 and with two k620 Quadro Nvidia graphic cards installed on it, and I had installed driver for the cards previously from the Ubuntu repository. Recently I installed the Cuda tool kit (available on the ubuntu repository). And I downloaded Cuda enabled namd 2.14 binary (Linux-x86_64-multicore-CUDA<;!!HXCxUKc!whuamcxuHUwWSpy-6s3lH0eNgn8-d_iqqViJTl5JZuNpWSN9uxfKOj6tWr72BaAuxwto8_9v57H5WyLtv50$> (NVIDIA CUDA acceleration). But when I am trying to run the simulation, I am getting the following error:

FATAL ERROR: CUDA error cudaMalloc(pp, sizeofT*(*curlen)) in file src/CudaUtils.C, function reallocate_device_T, line 130
 on Pe 0 (param-HP-Z440-Workstation device 0 pci 0:2:0): out of memory
[Partition 0][Node 0] End of program

I am using the following command to run the simulation.

namd2 +idlepoll benchmark_gpu.conf > benchmark_gpu.log

Please help me to sort out this error.

thanks in advance


This archive was generated by hypermail 2.1.6 : Tue Dec 13 2022 - 14:32:44 CST