Hi Ross,
Thanks for the pointer to simpleP2P. That illustrated the problem well enough to identify and fix a pci-bridge setting that somehow
became unset. We have also updated to the current Nvidia driver version 352.79
All is well now, both with simpleP2P and amber.
Sarah
On 2/12/16 7:03 PM, Ross Walker wrote:
> Hi Sarah,
>
> This is most likely a hardware configuration issue. There are a lot of vendors out there shipping misconfigured bios's with Haswell systems right now. I am guessing these are Haswell (v3) CPUs yes?
>
> As well as the output of the lspci command can you try building simpleP2P from the NVIDIA CUDA Samples and run it with the various combinations of GPUs.
>
> E.g.
> unset CUDA_VISIBLE_DEVICES
> ./simpleP2P
>
> export CUDA_VISIBLE_DEVICES=0,1
> ./simpleP2P
>
> export CUDA_VISIBLE_DEVICES=0,2
> ./simpleP2P
>
> export CUDA_VISIBLE_DEVICES=0,3
> ./simpleP2P
>
> export CUDA_VISIBLE_DEVICES=1,2
> ./simpleP2P
>
> export CUDA_VISIBLE_DEVICES=1,3
> ./simpleP2P
>
> export CUDA_VISIBLE_DEVICES=2,3
> ./simpleP2P
>
> I suspect various combinations here will report that they can do P2P communication but will fail the test.
>
> All the best
> Ross
>
>> On Feb 12, 2016, at 16:58, Sarah Anderson <saraha.cray.com> wrote:
>>
>> Hi Ross,
>>> Checking for updates...
>>> Checking for available patches online. This may take a few seconds...
>>>
>>> Available AmberTools 15 patches:
>>>
>>> No patches available
>>>
>>> Available Amber 14 patches:
>>>
>>> No patches available
>> Tried
>> openmpi/1.8.4_gcc 2) cudatoolkit/7.5.18 3) gcc/4.9.1
>>
>> The single-GPU configure -mpi -cuda -noX11 gnu
>> worked fine, but two-GPUs produced the same error.
>>> gpu_allreduce cudaDeviceSynchronize failed an illegal memory access was encountered
>>> srun: error: prd2-0171: task 0: Exited with exit code 255
>> I tried a MPI only gnu build, which worked fine with 16 or 32 ranks.
>>
>> I dropped back to cudatoolkit/7.0.28
>> Same message. I'm out of ideas for now. When I have the output of
>>> lspci -d "10b5:*" -vvv | grep ACSCtl
>> I'll send it to you.
>>
>> Sarah
>>
>>
>> On 2/12/16 4:36 PM, Ross Walker wrote:
>>> Hi Sarah,
>>>
>>> I suspect this is indeed an MPI issue - likely related to it screwing up how P2P communication works - but it could also be a bios issue or a compiler issue - again related to peer to peer communication. I've seen race conditions in a few of the Intel compiler versions but never been able to track it down and concluded it was a compiler bug. Can you check a couple of things please:
>>>
>>> 1) Make sure all the latest updates are applied.
>>>
>>> 2) Build with the GNU compilers and see if the problem is still there.
>>>
>>> Also the output from the following command would be useful in determining if it is a bios bug on the hardware or not:
>>>
>>> lspci -d "10b5:*" -vvv | grep ACSCtl
>>>
>>> (But it unfortunately needs to be run as root).
>>>
>>> All the best
>>> Ross
>>>
>>>> On Feb 12, 2016, at 14:24, Sarah Anderson<saraha.cray.com> wrote:
>>>>
>>>> Hi Ross,
>>>>
>>>> I was running this test:
>>>>
>>>> Amber14_Benchmark_Suite/PME/JAC_production_NVE
>>>>
>>>> srun -n 2 --mpi=pmi2 --cpu_bind=socket $AMBERHOME/bin/pmemd.cuda.MPI -O -i mdin.GPU -o mdout.2GPU -p prmtop -c inpcrd
>>>>
>>>> Yes, a single GPU run completes normally.
>>>>
>>>> I tried another test in that suite, and though the 2GPU test completed, it came up with different (nonsense) answers.
>>>> Maybe there's something wrong with the MPI/build. It's just Intel impi & "configure -cuda -mpi -noX11 intel"
>>>>
>>>> Thanks,
>>>> Sarah
>>>>
>>>> Two GPUs
>>>>
>>>> R M S F L U C T U A T I O N S
>>>>
>>>>
>>>> NSTEP = 1000 TIME(PS) = 102.000 TEMP(K) = 6.13 PRESS = 0.0
>>>> Etot = 10445.2658 EKtot = 388.9169 EPtot = 10213.0555
>>>> BOND = 138.3458 ANGLE = 184.8487 DIHED = 119.1381
>>>> 1-4 NB = 35.9507 1-4 EEL = 842.2853 VDWAALS = 9138.2936
>>>> EELEC = 2970.4534 EGB = 3580.7687 RESTRAINT = 0.0000
>>>> ------------------------------------------------------------------------------
>>>>
>>>>
>>>>
>>>> Single GPU:
>>>>
>>>> R M S F L U C T U A T I O N S
>>>>
>>>>
>>>> NSTEP = 1000 TIME(PS) = 102.000 TEMP(K) = 0.91 PRESS = 0.0
>>>> Etot = 22.9288 EKtot = 57.4768 EPtot = 49.0089
>>>> BOND = 32.3643 ANGLE = 82.1033 DIHED = 80.2520
>>>> 1-4 NB = 14.6668 1-4 EEL = 107.9454 VDWAALS = 148.9948
>>>> EELEC = 280.7436 EGB = 212.3126 RESTRAINT = 0.0000
>>>> ------------------------------------------------------------------------------
>>>>
>>>>
>>>>
>>>>
>>>> On 2/12/16 1:16 PM, Ross Walker wrote:
>>>>> Hi Sarah,
>>>>>
>>>>> The error message doesn't tell a lot here unfortunately. The issue with GPU error messages is that if you have an array in memory that contains a NAN - say the force array got an infinite force - then things will be fine 'until' the code tries to upload or download from the GPU (or do a similar copy operation) - NAN's are not supported in these operations and thus you get the error that you see. The real error - e.g. 2 atoms sitting on top of each other occurred somewhere else entirely within the code. The net result is that just because the error is in the gpu_allreduce does not mean it is related to something wrong with the GPUs, or a driver issue or even a multi-GPU issue.
>>>>>
>>>>> What it likely means there is something wrong with the simulation itself that you are running. Have you tried running on just 1 GPU and see if that crashes as well (and also CPU?). Can you provide some more details about what you are actually simulating.
>>>>>
>>>>> All the best
>>>>> Ross
>>>>>
>>>>>> On Feb 12, 2016, at 10:42, Sarah Anderson<saraha.cray.com> wrote:
>>>>>>
>>>>>> Has anyone seen this message lately? I saw some notes about in mid 2015 but no particular fix suggested.
>>>>>>
>>>>>> This is with cuda 7.5 using a pair of K80 GPUS in peer-to-peer mode.
>>>>>>
>>>>>> It fails with all combinations of CUDA_VISIBLE_DEVICES 0,1 2,3
>>>>>>
>>>>>>> gpu_allreduce cudaDeviceSynchronize failed an illegal memory access was encountered
>>>>>> |------------------- GPU DEVICE INFO --------------------
>>>>>> |
>>>>>> | Task ID: 0
>>>>>> | CUDA_VISIBLE_DEVICES: 0,1
>>>>>> | CUDA Capable Devices Detected: 2
>>>>>> | CUDA Device ID in use: 0
>>>>>> | CUDA Device Name: Tesla K80
>>>>>> | CUDA Device Global Mem Size: 11519 MB
>>>>>> | CUDA Device Num Multiprocessors: 13
>>>>>> | CUDA Device Core Freq: 0.82 GHz
>>>>>> |
>>>>>> |
>>>>>> | Task ID: 1
>>>>>> | CUDA_VISIBLE_DEVICES: 0,1
>>>>>> | CUDA Capable Devices Detected: 2
>>>>>> | CUDA Device ID in use: 1
>>>>>> | CUDA Device Name: Tesla K80
>>>>>> | CUDA Device Global Mem Size: 11519 MB
>>>>>> | CUDA Device Num Multiprocessors: 13
>>>>>> | CUDA Device Core Freq: 0.82 GHz
>>>>>> |
>>>>>> |--------------------------------------------------------
>>>>>>
>>>>>> |---------------- GPU PEER TO PEER INFO -----------------
>>>>>> |
>>>>>> | Peer to Peer support: ENABLED
>>>>>> |
>>>>>> |--------------------------------------------------------
>>>>>>
>>>>>>
>>>>>> Here is deviceQuery
>>>>>>
>>>>>> CUDA Device Query (Runtime API) version (CUDART static linking)
>>>>>>
>>>>>> Detected 2 CUDA Capable device(s)
>>>>>>
>>>>>> Device 0: "Tesla K80"
>>>>>> CUDA Driver Version / Runtime Version 7.5 / 7.5
>>>>>> CUDA Capability Major/Minor version number: 3.7
>>>>>> Total amount of global memory: 11520 MBytes (12079136768 bytes)
>>>>>> MapSMtoCores for SM 3.7 is undefined. Default to use 192 Cores/SM
>>>>>> MapSMtoCores for SM 3.7 is undefined. Default to use 192 Cores/SM
>>>>>> (13) Multiprocessors, (192) CUDA Cores/MP: 2496 CUDA Cores
>>>>>> GPU Clock rate: 824 MHz (0.82 GHz)
>>>>>> Memory Clock rate: 2505 Mhz
>>>>>> Memory Bus Width: 384-bit
>>>>>> L2 Cache Size: 1572864 bytes
>>>>>> Maximum Texture Dimension Size (x,y,z) 1D=(65536), 2D=(65536, 65536), 3D=(4096, 4096, 4096)
>>>>>> Maximum Layered 1D Texture Size, (num) layers 1D=(16384), 2048 layers
>>>>>> Maximum Layered 2D Texture Size, (num) layers 2D=(16384, 16384), 2048 layers
>>>>>> Total amount of constant memory: 65536 bytes
>>>>>> Total amount of shared memory per block: 49152 bytes
>>>>>> Total number of registers available per block: 65536
>>>>>> Warp size: 32
>>>>>> Maximum number of threads per multiprocessor: 2048
>>>>>> Maximum number of threads per block: 1024
>>>>>> Max dimension size of a thread block (x,y,z): (1024, 1024, 64)
>>>>>> Max dimension size of a grid size (x,y,z): (2147483647, 65535, 65535)
>>>>>> Maximum memory pitch: 2147483647 bytes
>>>>>> Texture alignment: 512 bytes
>>>>>> Concurrent copy and kernel execution: Yes with 2 copy engine(s)
>>>>>> Run time limit on kernels: No
>>>>>> Integrated GPU sharing Host Memory: No
>>>>>> Support host page-locked memory mapping: Yes
>>>>>> Alignment requirement for Surfaces: Yes
>>>>>> Device has ECC support: Enabled
>>>>>> Device supports Unified Addressing (UVA): Yes
>>>>>> Device PCI Bus ID / PCI location ID: 5 / 0
>>>>>> Compute Mode:
>>>>>> < Default (multiple host threads can use ::cudaSetDevice() with device simultaneously) >
>>>>>>
>>>>>> Device 1: "Tesla K80"
>>>>>> CUDA Driver Version / Runtime Version 7.5 / 7.5
>>>>>> CUDA Capability Major/Minor version number: 3.7
>>>>>> Total amount of global memory: 11520 MBytes (12079136768 bytes)
>>>>>> MapSMtoCores for SM 3.7 is undefined. Default to use 192 Cores/SM
>>>>>> MapSMtoCores for SM 3.7 is undefined. Default to use 192 Cores/SM
>>>>>> (13) Multiprocessors, (192) CUDA Cores/MP: 2496 CUDA Cores
>>>>>> GPU Clock rate: 824 MHz (0.82 GHz)
>>>>>> Memory Clock rate: 2505 Mhz
>>>>>> Memory Bus Width: 384-bit
>>>>>> L2 Cache Size: 1572864 bytes
>>>>>> Maximum Texture Dimension Size (x,y,z) 1D=(65536), 2D=(65536, 65536), 3D=(4096, 4096, 4096)
>>>>>> Maximum Layered 1D Texture Size, (num) layers 1D=(16384), 2048 layers
>>>>>> Maximum Layered 2D Texture Size, (num) layers 2D=(16384, 16384), 2048 layers
>>>>>> Total amount of constant memory: 65536 bytes
>>>>>> Total amount of shared memory per block: 49152 bytes
>>>>>> Total number of registers available per block: 65536
>>>>>> Warp size: 32
>>>>>> Maximum number of threads per multiprocessor: 2048
>>>>>> Maximum number of threads per block: 1024
>>>>>> Max dimension size of a thread block (x,y,z): (1024, 1024, 64)
>>>>>> Max dimension size of a grid size (x,y,z): (2147483647, 65535, 65535)
>>>>>> Maximum memory pitch: 2147483647 bytes
>>>>>> Texture alignment: 512 bytes
>>>>>> Concurrent copy and kernel execution: Yes with 2 copy engine(s)
>>>>>> Run time limit on kernels: No
>>>>>> Integrated GPU sharing Host Memory: No
>>>>>> Support host page-locked memory mapping: Yes
>>>>>> Alignment requirement for Surfaces: Yes
>>>>>> Device has ECC support: Enabled
>>>>>> Device supports Unified Addressing (UVA): Yes
>>>>>> Device PCI Bus ID / PCI location ID: 6 / 0
>>>>>> Compute Mode:
>>>>>> < Default (multiple host threads can use ::cudaSetDevice() with device simultaneously) >
>>>>>>> Peer access from Tesla K80 (GPU0) -> Tesla K80 (GPU1) : Yes
>>>>>>> Peer access from Tesla K80 (GPU1) -> Tesla K80 (GPU0) : Yes
>>>>>> deviceQuery, CUDA Driver = CUDART, CUDA Driver Version = 7.5, CUDA Runtime Version = 7.5, NumDevs = 2, Device0 = Tesla K80, Device1
>>>>>> = Tesla K80
>>>>>> Result = PASS
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
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>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>> _______________________________________________
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Received on Mon Feb 15 2016 - 09:30:02 PST
