Hello! I'm currently trying to install Amber22 with AmberTools23 on our Debian 11 cluster.
Steps 1-5 of the installation according to the manual worked fine, resulting in only 4 Errors (4 of which could be ignored) in the make test.serial step.
When trying to proceed with step 7 I get
0 file comparisons passed
0 file comparisons failed
247 tests experienced errors
from the make test.cuda.serial, all looking pretty much exactly like this:
Segmentation fault
./Run: Program error
make[3]: [Makefile:403: test.pmemd.cuda.gti.others] Error 1 (ignored)
make[3]: Leaving directory '/media/local/softwareMCD/amber/amber22/test/cuda'
export TESTsander=/media/local/softwareMCD/amber/amber22///bin/sander.quick.cuda; make -k test.sander.Quick
make[3]: Entering directory '/media/local/softwareMCD/amber/amber22/test'
Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
Backtrace for this error:
#0 0x7f26f981fbd0 in ???
#1 0x7f26f981ee25 in ???
#2 0x7f26f9664d5f in ???
at ./signal/../sysdeps/unix/sysv/linux/x86_64/sigaction.c:0
#3 0x7f26cc83bf0b in ???
#4 0x7f26cc7e9759 in ???
#5 0x7f26cc64d84f in ???
#6 0x7f26fa905397 in ???
#7 0x7f26f9add34e in __pthread_once_slow
at ./nptl/pthread_once.c:116
#8 0x7f26fa949308 in ???
#9 0x7f26fa901dc2 in ???
#10 0x7f26fa921370 in ???
#11 0x7f26fa8d3095 in ???
#12 0x7f26fa2aa3c4 in ???
#13 0x56144f113b14 in ???
#14 0x56144f113ec4 in ???
#15 0x56144f0b998b in ???
#16 0x56144ef5187a in ???
#17 0x56144efac65e in ???
#18 0x56144ef974ab in ???
#19 0x56144ef90399 in ???
#20 0x56144ef903f5 in ???
#21 0x7f26f964fd09 in __libc_start_main
at ../csu/libc-start.c:308
#22 0x56144edcd7d9 in ???
#23 0xffffffffffffffff in ???
Before the compilation of with -DCUDA=TRUE failed at 97% and I added the line
#define THRUST_IGNORE_CUB_VERSION_CHECK
to the very top of my xxxxx/amber/amber22_src/src/pmemd/src/cuda/kNLRadixSort.cu
Not sure if this is related but I thought I'd mention it
Please help us out with this problem
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Received on Fri May 19 2023 - 08:00:02 PDT
