This bug occurs for reading from stdin in C too.
Again on an exodar schroot on sid:
CONTEXT:
$ dpkg -l |egrep "tree.*puzzle|openmpi|pmix|gfortran|gcc|mpifort|libc[-0]"
ii gcc 4:8.2.0-2 hurd-i386
GNU C compiler
ii gcc-8 8.2.0-14 hurd-i386
GNU C compiler
ii gcc-8-base:hurd-i386 8.2.0-14 hurd-i386
GCC, the GNU Compiler Collection (base package)
ii gfortran 4:8.2.0-2 hurd-i386
GNU Fortran 95 compiler
ii gfortran-8 8.2.0-14 hurd-i386
GNU Fortran compiler
ii gromacs-openmpi 2018.4-1 hurd-i386
Molecular dynamics sim, binaries for OpenMPI parallelization
ii libc-bin 2.28-5 hurd-i386
GNU C Library: Binaries
ii libc-dev-bin 2.28-5 hurd-i386
GNU C Library: Development binaries
ii libc-l10n 2.28-5 all
GNU C Library: localization files
ii libc0.3:hurd-i386 2.28-5 hurd-i386
GNU C Library: Shared libraries
ii libc0.3-dev:hurd-i386 2.28-5 hurd-i386
GNU C Library: Development Libraries and Header Files
ii libgcc-8-dev:hurd-i386 8.2.0-14 hurd-i386
GCC support library (development files)
ii libgcc1:hurd-i386 1:8.2.0-14 hurd-i386
GCC support library
ii libgfortran-8-dev:hurd-i386 8.2.0-14 hurd-i386
Runtime library for GNU Fortran applications (development files)
ii libgfortran5:hurd-i386 8.2.0-14 hurd-i386
Runtime library for GNU Fortran applications
ii libopenmpi-dev:hurd-i386 3.1.3-9 hurd-i386
high performance message passing library -- header files
ii libopenmpi3:hurd-i386 3.1.3-9 hurd-i386
high performance message passing library -- shared library
ii libpmix2:hurd-i386 3.1.0~rc4-1 hurd-i386
Process Management Interface (Exascale) library
ii openmpi-bin 3.1.3-9 hurd-i386
high performance message passing library -- binaries
ii openmpi-common 3.1.3-9 all
high performance message passing library -- common files
ii tree-puzzle 5.2-11 hurd-i386
Reconstruction of phylogenetic trees by maximum likelihood
ii tree-puzzle-doc 5.2-11 all
Reconstruction of phylogenetic trees by maximum likelihood (doc)
$ mpicc --showme
gcc -I/usr/lib/i386-gnu/openmpi/include/openmpi
-I/usr/lib/i386-gnu/openmpi/include -pthread -L/usr/lib/i386-gnu/openmpi/lib
-lmpi
REPRODUCE THE BUG:
$ cat hurd_C_minimal.c
#include <stdio.h>
#include <strings.h>
int main(void){
int i = 178;
int j;
printf("i = %d\n",i);
scanf("%10d",&j);
printf("j = %d\n",j);
return 0;
}
$ cat infile
414
$ gcc hurd_C_minimal.c && time ./a.out < infile
i = 178
j = 414
real 0m0.010s
user 0m0.000s
sys 0m0.000s
$ mpicc src/hurd_C_minimal.c && (time mpirun -n 1 --mca plm_rsh_agent /bin/false
./a.out < infile ) &
[2] 21871
i = 178
Runs for at least 30 seconds cpu time at about 10% cpu before I killed it.
REPRODUCE THE BUG - tree-puzzle:
This bug should affect all other openmpi packages which read from stdin,
such as tree-puzzle 5.2-11:
Again on an exodar schroot on sid:
(0) prepare 2-line input file:
$ cp -pv /usr/share/doc/tree-puzzle/examples/primates.b .
$ printf "primates.b\ny\n" > infile.tree-puzzle
(1) without mpi
$ time tree-puzzle < infile.tree-puzzle > /dev/null && ls -lt out????
Using SPRNG -- Scalable Parallel Random Number Generator
WARNING from init_rng: Parameter not valid. Using Default param
real 0m0.020s
user 0m0.000s
sys 0m0.000s
-rw-r--r-- 1 boud-guest boud-guest 284 Jan 16 01:04 outdist
-rw-r--r-- 1 boud-guest boud-guest 7095 Jan 16 01:04 outfile
-rw-r--r-- 1 boud-guest boud-guest 130 Jan 16 01:04 outtree
(2) with mpi
$ (time mpirun -n 1 --mca plm_rsh_agent /bin/false tree-puzzle < infile.tree-puzzle >
/dev/null && ls -lt out????) &
[1] 13122
Using SPRNG -- Scalable Parallel Random Number Generator
WARNING from init_rng: Parameter not valid. Using Default param
Runs at about 10-20% of cpu for at least 80 seconds of cpu time.
