[gmx-users] GXM 512 allocation issue
Mark Abraham
mark.j.abraham at gmail.com
Mon Jul 4 14:32:14 CEST 2016
Hi,
Hmm that's a new one on me, too! How many particles has this system? Can
you please open an issue at
https://redmine.gromacs.org/projects/gromacs/issues/new and attach your
.tpr?
Mark
On Mon, Jul 4, 2016 at 2:16 PM Carlo Camilloni <carlo.camilloni at gmail.com>
wrote:
> Dear GMX users,
>
> the last week I began using a GPU cluster and I am now getting an error I
> have never seen before:
>
> 85 Source code file:
> /homea/hmu24/hmu240/Codes/gromacs/src/gromacs/utility/smalloc.c, line: 227
> 86
> 87 Fatal error:
> 88 Not enough memory. Failed to realloc 323880 bytes for sort->sort2,
> sort->sort2=67733e20
> 89 (called from file
> /homea/hmu24/hmu240/Codes/gromacs/src/gromacs/domdec/domdec.cpp, line 9215)
> 90 For more information and tips for troubleshooting, please check the
> GROMACS
>
> I am using GMX 5.1.2, these are the details of the architecture from the
> log file
> (i am running the simulation using 4 MPI + 6 OpenMP threads using 4 GPUs)
> the errors is trigger randomly.
>
> Is this also happening to others?
>
> Precision: single
> 38 Memory model: 64 bit
> 39 MPI library: MPI
> 40 OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 32)
> 41 GPU support: enabled
> 42 OpenCL support: disabled
> 43 invsqrt routine: gmx_software_invsqrt(x)
> 44 SIMD instructions: AVX2_256
> 45 FFT library: fftw-3.3.4-sse2-avx
> 46 RDTSCP usage: enabled
> 47 C++11 compilation: disabled
> 48 TNG support: enabled
> 49 Tracing support: disabled
> 50 Built on: Tue 21 Jun 21:34:57 CEST 2016
> 51 Built by: hmu240 at jrl03 [CMAKE]
> 52 Build OS/arch: Linux 3.10.0-327.18.2.el7.x86_64 x86_64
> 53 Build CPU vendor: GenuineIntel
> 54 Build CPU brand: Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz
> 55 Build CPU family: 6 Model: 63 Stepping: 2
> 56 Build CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma
> htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd
> rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
> 57 C compiler: /usr/bin/cc GNU 4.8.5
> 58 C compiler flags: -march=core-avx2 -Wextra
> -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall
> -Wno-unused -Wunused-value -Wunused-parameter -O3 -DNDEBUG
> -funroll-all-loop s -fexcess-precision=fast -Wno-array-bounds
> 59 C++ compiler: /usr/bin/c++ GNU 4.8.5
> 60 C++ compiler flags: -march=core-avx2 -Wextra
> -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function
> -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-array-bound
> s
> 61 Boost version: 1.55.0 (internal)
> 62 CUDA compiler:
> /usr/local/software/jureca/Stages/2016a/software/CUDA/7.5.18-iccifort-2015.3.187-GCC-4.9.3-2.25/bin/nvcc
> nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2015 NVIDIA Corp
> oration;Built on Tue_Aug_11_14:27:32_CDT_2015;Cuda compilation tools,
> release 7.5, V7.5.17
> 63 CUDA compiler
> flags:-gencode;arch=compute_20,code=sm_20;-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_50,code=sm_5
>
> 0;-gencode;arch=compute_52,code=sm_52;-gencode;arch=compute_52,code=compute_52;-use_fast_math;;
> ;-march=core-avx2;-Wextra;-Wno-missing-field-initializers;-Wpointer-arith;-Wall;-Wno-unused-function;-
>
> O3;-DNDEBUG;-funroll-all-loops;-fexcess-precision=fast;-Wno-array-bounds;
> 64 CUDA driver: 7.50
> 65 CUDA runtime: 7.50
> 66
> 67
> 68 Number of logical cores detected (48) does not match the number
> reported by OpenMP (6).
> 69 Consider setting the launch configuration manually!
> 70
> 71 Running on 1 node with total 24 cores, 48 logical cores, 4
> compatible GPUs
> 72 Hardware detected on host jrc0489 (the node of MPI rank 0):
> 73 CPU info:
> 74 Vendor: GenuineIntel
> 75 Brand: Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz
> 76 Family: 6 model: 63 stepping: 2
> 77 CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt
> lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd
> rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
> 78 SIMD instructions most likely to fit this hardware: AVX2_256
> 79 SIMD instructions selected at GROMACS compile time: AVX2_256
> 80 GPU info:
> 81 Number of GPUs detected: 4
> 82 #0: NVIDIA Tesla K80, compute cap.: 3.7, ECC: yes, stat:
> compatible
> 83 #1: NVIDIA Tesla K80, compute cap.: 3.7, ECC: yes, stat:
> compatible
> 84 #2: NVIDIA Tesla K80, compute cap.: 3.7, ECC: yes, stat:
> compatible
> 85 #3: NVIDIA Tesla K80, compute cap.: 3.7, ECC: yes, stat:
> compatible
>
>
> Best regards,
> Carlo
>
>
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