I am attempting to install AMBER with GPU support on a new computing
cluster. Unfortunately, when it attempts to install pbsa, I get the
following error (apparently our gcc compiler is too... new?):
/cm/shared/apps/cuda10.2/toolkit/10.2.89/bin/nvcc -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_50 -gencode
> arch=compute_52,code=sm_52 -gencode arch=compute_53,code=sm_53 -gencode
> arch=compute_60,code=sm_60 -gencode arch=compute_61,code=sm_61 -gencode
> arch=compute_60,code=sm_70, -gencode arch=compute_61,code=sm_70
> -Wno-deprecated-declarations -use_fast_math -O3 -ccbin g++ -o
> cuda_mg_wrapper.o -c cuda_mg_wrapper.cu
> In file included from
> /cm/shared/apps/cuda10.2/toolkit/10.2.89/bin/../targets/x86_64-linux/include/cuda_runtime.h:83,
> from <command-line>:
> /cm/shared/apps/cuda10.2/toolkit/10.2.89/bin/../targets/x86_64-linux/include/crt/host_config.h:138:2:
> error: #error -- unsupported GNU version! gcc versions later than 8 are not
> supported!
> 138 | #error -- unsupported GNU version! gcc versions later than 8 are
> not supported!
> | ^~~~~
> make[2]: *** [cuda_mg_wrapper.o] Error 1
> make[2]: Leaving directory `/home/wesley/amber18/AmberTools/src/pbsa'
> make[1]: *** [cuda_serial] Error 2
> make[1]: Leaving directory `/home/wesley/amber18/AmberTools/src'
> make: *** [install] Error 2
This is on a new rack server from Bright Computing. Although it comes with
amber20 installed, we are attempting to trouble shoot some errors we saw
trying to run a system between amber18 and amber20 elsewhere.
Amber was configured using './configure -cuda gnu'
The serial code (single cpu, i.e. ./configure gnu) was able to compile and
install without error and all test cases passed, including pbsa... so this
seems to be something specific to the GPU code.
Below is relevant information about our hardware, compilers, etc.
> $ uname -a
> Linux bright90 3.10.0-1127.10.1.el7.x86_64 #1 SMP Wed Jun 3 14:28:03 UTC
> 2020 x86_64 x86_64 x86_64 GNU/Linux
gcc version 9.2.0 (GCC)
$ nvcc --version
> nvcc: NVIDIA (R) Cuda compiler driver
> Copyright (c) 2005-2019 NVIDIA Corporation
> Built on Wed_Oct_23_19:24:38_PDT_2019
> Cuda compilation tools, release 10.2, V10.2.89
$ lscpu
> Architecture: x86_64
> CPU op-mode(s): 32-bit, 64-bit
> Byte Order: Little Endian
> CPU(s): 40
> On-line CPU(s) list: 0-39
> Thread(s) per core: 2
> Core(s) per socket: 10
> Socket(s): 2
> NUMA node(s): 2
> Vendor ID: GenuineIntel
> CPU family: 6
> Model: 85
> Model name: Intel(R) Xeon(R) Silver 4210 CPU . 2.20GHz
> Stepping: 7
> CPU MHz: 1000.097
> CPU max MHz: 3200.0000
> CPU min MHz: 1000.0000
> BogoMIPS: 4400.00
> Virtualization: VT-x
> L1d cache: 32K
> L1i cache: 32K
> L2 cache: 1024K
> L3 cache: 14080K
> NUMA node0 CPU(s): 0-9,20-29
> NUMA node1 CPU(s): 10-19,30-39
> Flags: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr
> pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe
> syscall nx pdpe1gb rdtscp lm constant_tsc art arch_perfmon pebs bts
> rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq
> dtes64 monitor ds_cpl vmx smx est tm2 ssse3 sdbg fma cx16 xtpr pdcm pcid
> dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c
> rdrand lahf_lm abm 3dnowprefetch epb cat_l3 cdp_l3 invpcid_single
> intel_ppin intel_pt ssbd mba ibrs ibpb stibp ibrs_enhanced tpr_shadow vnmi
> flexpriority ept vpid fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms
> invpcid rtm cqm mpx rdt_a avx512f avx512dq rdseed adx smap clflushopt clwb
> avx512cd avx512bw avx512vl xsaveopt xsavec xgetbv1 cqm_llc cqm_occup_llc
> cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts pku ospke avx512_vnni
> md_clear spec_ctrl intel_stibp flush_l1d arch_capabilities
Anyone know how to fix this error? I would perfer not having to install a
separate, older, version of GCC just to run amber18 if possible as this
could lead to a lot of complications since all our system library files
seem to be compiled using the newer gcc...
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Received on Thu Oct 22 2020 - 12:00:02 PDT
