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.