Hello, Amber community
I was running minimization following the tutorial available at
https://ambermd.org/tutorials/basic/tutorial1/section5.php. Stage 1
minimization (Holding the solute fixed) running successfully without any
error but the stage 2 minimization gives the error below.
sander -O -i min2.in -o min2.out -p lassa_ion.prmtop -c min1.ncrst -r
min2.ncrst
Program received signal SIGSEGV: Segmentation fault - invalid memory
reference.
Backtrace for this error:
#0 0x7f1dd5eb6d01 in ???
#1 0x7f1dd5eb5ed5 in ???
#2 0x7f1dd5ccf20f in ???
#3 0x55b088ac55d2 in ???
#4 0x55b088ac7c3c in ???
#5 0x55b088a06a7f in ???
#6 0x55b088a5f59b in ???
#7 0x55b088a4b8a9 in ???
#8 0x55b088a4482c in ???
#9 0x55b088a44888 in ???
#10 0x7f1dd5cb00b2 in ???
#11 0x55b08888ed3d in ???
#12 0xffffffffffffffff in ???
Segmentation fault (core dumped).
During installation, I built the CPU serial version first and run "make
test.serial" All the tests were passed, thereafter I build GPU serial
version which was successful as no error was reported during installation.
I then run
cd $AMBERHOME; make test.serial.cuda and get
make: *** No rule to make target 'test.serial.cuda'. Stop.
I also tried
cd $AMBERHOME;
export CUDA_VISIBLE_DEVICES=2
make test.cuda.serial and get
(cd AmberTools/test && make test.cuda.serial)
make[1]: Entering directory
'/home/akinyemi/Downloads/Amber20/amber20/AmberTools/test'
Makefile:2: /config.h: No such file or directory
make[1]: *** No rule to make target '/config.h'. Stop.
make[1]: Leaving directory
'/home/akinyemi/Downloads/Amber20/amber20/AmberTools/test'
make: [Makefile:40: test.cuda.serial] Error 2 (ignored)
(cd test && make test.cuda.serial)
make[1]: Entering directory '/home/akinyemi/Downloads/Amber20/amber20/test'
Makefile:4: /config.h: No such file or directory
make[1]: *** No rule to make target '/config.h'. Stop.
make[1]: Leaving directory '/home/akinyemi/Downloads/Amber20/amber20/test'
make: [Makefile:41: test.cuda.serial] Error 2 (ignored).
Please help
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Received on Sat Jun 05 2021 - 06:30:02 PDT
