You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
I am going to follow the tutorial to use the anphon, but I am getting the following error. May I ask how to solve this?
&general
PREFIX = STO444
MODE = phonons
FCSXML = STO444.xml
NKD = 3; KD = Sr Ti O
/
&cell
7.55890449850308 # factor in Bohr unit
3.8957417004200208 0.0000000000000000 0.0000000000000000
0.0000000000000000 3.8957417004200208 0.0000000000000000
0.0000000000000000 0.0000000000000000 3.8957417004200208
/
&kpoint
1
G 0.0 0.0 0.0 X 0.5 0.0 0.0 51
X 0.5 0.0 0.0 M 0.5 0.5 0.0 51
M 0.5 0.5 0.0 G 0.0 0.0 0.0 51
G 0.0 0.0 0.0 R 0.5 0.5 0.5 51
R 0.5 0.5 0.5 M 0.5 0.5 0.0 51
/
$ anphon STO_alm2.in > STO_alm2.log
[mee2322:2355704] shmem: mmap: an error occurred while determining whether or not /tmp/ompi.mee2322.1000/jf.0/164102144/shared_mem_cuda_pool.mee2322 could be created.
[mee2322:2355704] create_and_attach: unable to create shared memory BTL coordinating structure :: size 134217728
[mee2322:2355704:0:2355704] Caught signal 11 (Segmentation fault: address not mapped to object at address 0x440000e0)
==== backtrace (tid:2355704) ====
0 /lib/x86_64-linux-gnu/libucs.so.0(ucs_handle_error+0x2e4) [0x11642e8e1fc4]
1 /lib/x86_64-linux-gnu/libucs.so.0(+0x24fec) [0x11642e8e5fec]
2 /lib/x86_64-linux-gnu/libucs.so.0(+0x251aa) [0x11642e8e61aa]
3 /home/user/anaconda3/envs/alamode/lib/libmpi.so.40(MPI_Comm_rank+0x33) [0x11642fb04b03]
4 anphon(_ZN7PHON_NS5MyMPIC1EPNS_4PHONEi+0x12b) [0x56203674a81b]
5 anphon(_ZN7PHON_NS4PHONC1EiPPci+0x74) [0x562036769674]
6 anphon(main+0x40) [0x5620366ae830]
7 /lib/x86_64-linux-gnu/libc.so.6(+0x29d90) [0x11642f029d90]
8 /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80) [0x11642f029e40]
9 anphon(+0x388d1) [0x5620366ae8d1]
[mee2322:2355704] *** Process received signal ***
[mee2322:2355704] Signal: Segmentation fault (11)
[mee2322:2355704] Signal code: (-6)
[mee2322:2355704] Failing at address: 0x3e80023f1f8
[mee2322:2355704] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x42520)[0x11642f042520]
[mee2322:2355704] [ 1] /home/user/anaconda3/envs/alamode/lib/libmpi.so.40(MPI_Comm_rank+0x33)[0x11642fb04b03]
[mee2322:2355704] [ 2] anphon(_ZN7PHON_NS5MyMPIC1EPNS_4PHONEi+0x12b)[0x56203674a81b]
[mee2322:2355704] [ 3] anphon(_ZN7PHON_NS4PHONC1EiPPci+0x74)[0x562036769674]
[mee2322:2355704] [ 4] anphon(main+0x40)[0x5620366ae830]
[mee2322:2355704] [ 5] /lib/x86_64-linux-gnu/libc.so.6(+0x29d90)[0x11642f029d90]
[mee2322:2355704] [ 6] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80)[0x11642f029e40]
[mee2322:2355704] [ 7] anphon(+0x388d1)[0x5620366ae8d1]
[mee2322:2355704] *** End of error message ***
Segmentation fault (core dumped)
reacted with thumbs up emoji reacted with thumbs down emoji reacted with laugh emoji reacted with hooray emoji reacted with confused emoji reacted with heart emoji reacted with rocket emoji reacted with eyes emoji
-
I am going to follow the tutorial to use the anphon, but I am getting the following error. May I ask how to solve this?
&general
PREFIX = STO444
MODE = phonons
FCSXML = STO444.xml
NKD = 3; KD = Sr Ti O
/
&cell
7.55890449850308 # factor in Bohr unit
3.8957417004200208 0.0000000000000000 0.0000000000000000
0.0000000000000000 3.8957417004200208 0.0000000000000000
0.0000000000000000 0.0000000000000000 3.8957417004200208
/
&kpoint
1
G 0.0 0.0 0.0 X 0.5 0.0 0.0 51
X 0.5 0.0 0.0 M 0.5 0.5 0.0 51
M 0.5 0.5 0.0 G 0.0 0.0 0.0 51
G 0.0 0.0 0.0 R 0.5 0.5 0.5 51
R 0.5 0.5 0.5 M 0.5 0.5 0.0 51
/
$ anphon STO_alm2.in > STO_alm2.log
[mee2322:2355704] shmem: mmap: an error occurred while determining whether or not /tmp/ompi.mee2322.1000/jf.0/164102144/shared_mem_cuda_pool.mee2322 could be created.
[mee2322:2355704] create_and_attach: unable to create shared memory BTL coordinating structure :: size 134217728
[mee2322:2355704:0:2355704] Caught signal 11 (Segmentation fault: address not mapped to object at address 0x440000e0)
==== backtrace (tid:2355704) ====
0 /lib/x86_64-linux-gnu/libucs.so.0(ucs_handle_error+0x2e4) [0x11642e8e1fc4]
1 /lib/x86_64-linux-gnu/libucs.so.0(+0x24fec) [0x11642e8e5fec]
2 /lib/x86_64-linux-gnu/libucs.so.0(+0x251aa) [0x11642e8e61aa]
3 /home/user/anaconda3/envs/alamode/lib/libmpi.so.40(MPI_Comm_rank+0x33) [0x11642fb04b03]
4 anphon(_ZN7PHON_NS5MyMPIC1EPNS_4PHONEi+0x12b) [0x56203674a81b]
5 anphon(_ZN7PHON_NS4PHONC1EiPPci+0x74) [0x562036769674]
6 anphon(main+0x40) [0x5620366ae830]
7 /lib/x86_64-linux-gnu/libc.so.6(+0x29d90) [0x11642f029d90]
8 /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80) [0x11642f029e40]
9 anphon(+0x388d1) [0x5620366ae8d1]
[mee2322:2355704] *** Process received signal ***
[mee2322:2355704] Signal: Segmentation fault (11)
[mee2322:2355704] Signal code: (-6)
[mee2322:2355704] Failing at address: 0x3e80023f1f8
[mee2322:2355704] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x42520)[0x11642f042520]
[mee2322:2355704] [ 1] /home/user/anaconda3/envs/alamode/lib/libmpi.so.40(MPI_Comm_rank+0x33)[0x11642fb04b03]
[mee2322:2355704] [ 2] anphon(_ZN7PHON_NS5MyMPIC1EPNS_4PHONEi+0x12b)[0x56203674a81b]
[mee2322:2355704] [ 3] anphon(_ZN7PHON_NS4PHONC1EiPPci+0x74)[0x562036769674]
[mee2322:2355704] [ 4] anphon(main+0x40)[0x5620366ae830]
[mee2322:2355704] [ 5] /lib/x86_64-linux-gnu/libc.so.6(+0x29d90)[0x11642f029d90]
[mee2322:2355704] [ 6] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80)[0x11642f029e40]
[mee2322:2355704] [ 7] anphon(+0x388d1)[0x5620366ae8d1]
[mee2322:2355704] *** End of error message ***
Segmentation fault (core dumped)
Beta Was this translation helpful? Give feedback.
All reactions