help compiling silo 4.10.2 on ubuntu 20.04 lts x86_64

[markcmiller86]

Date: Thu, 17 Dec 2020 16:25:03 -0800
From: wphan at vols.utk.edu (Phan, Wileam)
This post was imported from the visit-users@ornl.gov email archive

---

Hi,

I'm trying to compile SILO 4.10.2 from the tarball downloaded from
https://wci.llnl.gov/simulation/computer-codes/silo/downloads
with the default GCC version (9.3.0) from Ubuntu repositories for
Ubuntu 20.04.1 LTS.

I'm using LibAEC (SZIP replacement) 1.0.4 from
https://gitlab.dkrz.de/k202009/libaec,
and HDF5 1.12.0 (compiled from source, in serial mode).

SILO build crashes with the following error:

silo_hdf5.c: In function ?db_hdf5_process_file_options?:
silo_hdf5.c:4667:2: warning: #warning REMOVED WINDOWS SPECIFIC CHECK [-
Wcpp]
4667 | #warning REMOVED WINDOWS SPECIFIC CHECK
|  ^''''''
silo_hdf5.c:4808:2: warning: #warning REMOVED WINDOWS SPECIFIC CHECK [-
Wcpp]
4808 | #warning REMOVED WINDOWS SPECIFIC CHECK
|  ^''''''
silo_hdf5.c: In function ?db_hdf5_initiate_close?:
silo_hdf5.c:5442:47: warning: format ?%d? expects argument of type
?int?, but argument 4 has type ?hid_t? {aka ?long int?} [-Wformat=]
5442 |                 sprintf(tmp, ' '%.235s ' (id=%d), ', name,
ooids[i]);
|                                              ~^            '''~
'''~
|                                               |
|
|                                               int
hid_t {aka long int}
|                                              %ld
In file included from /opt/hdf5/hdf5-1.12.0/gcc-
9.3.0/include/H5public.h:32,
from /opt/hdf5/hdf5-1.12.0/gcc-
9.3.0/include/hdf5.h:22,
from silo_hdf5_private.h:71,
from silo_hdf5.c:72:
silo_hdf5.c: In function ?db_hdf5_SortObjectsByOffset?:
silo_hdf5.c:15779:18: error: too few arguments to function
?H5Oget_info3?
15779 |                  H5Oget_info(oid, &oinfo)<0 ||
|                  ^'''''''''~
In file included from /opt/hdf5/hdf5-1.12.0/gcc-
9.3.0/include/H5Apublic.h:22,
from /opt/hdf5/hdf5-1.12.0/gcc-
9.3.0/include/hdf5.h:23,
from silo_hdf5_private.h:71,
from silo_hdf5.c:72:
/opt/hdf5/hdf5-1.12.0/gcc-9.3.0/include/H5Opublic.h:187:15: note:
declared here
187 | H5_DLL herr_t H5Oget_info3(hid_t loc_id, H5O_info2_t *oinfo,
unsigned fields);
|               ^'''''''''~~
silo_hdf5.c:15783:38: error: ?H5O_info2_t? {aka ?struct H5O_info2_t?}
has no member named ?addr?
15783 |                 iop[i].offset = oinfo.addr;
|                                      ^
mv -f .deps/H5FDsilo.Tpo .deps/H5FDsilo.Plo
make[4]: *** [Makefile:386: silo_hdf5.lo] Error 1

---

Attached are the config files and build logs for all three libraries.

Some system info:

$ uname -a
Linux basecamp 5.4.0-58-generic #64-Ubuntu SMP Wed Dec 9 08:16:25 UTC
2020 x86_64 x86_64 x86_64 GNU/Linux

$ lsb_release -a
LSB Version:    core-11.1.0ubuntu2-noarch:printing-11.1.0ubuntu2-
noarch:security-11.1.0ubuntu2-noarch
Distributor ID: Ubuntu
Description:    Ubuntu 20.04.1 LTS
Release:        20.04
Codename:       focal

$ ompi_info
Package: Open MPI wyp at basecamp Distribution
Open MPI: 4.0.4
Open MPI repo revision: v4.0.4
Open MPI release date: Jun 10, 2020
Open RTE: 4.0.4
Open RTE repo revision: v4.0.4
Open RTE release date: Jun 10, 2020
OPAL: 4.0.4
OPAL repo revision: v4.0.4
OPAL release date: Jun 10, 2020
MPI API: 3.1.0
Ident string: 4.0.4
Prefix: /opt/mpi/gcc-9.3.0/openmpi-4.0.4/nocuda
Configured architecture: x86_64-unknown-linux-gnu
Configure host: basecamp
Configured by: wyp
Configured on: Fri Jul 17 20:19:52 EDT 2020
Configure host: basecamp
Configure command line: '--prefix=/opt/mpi/gcc-9.3.0/openmpi-
4.0.4/nocuda'
Built by: wyp
Built on: Fri 17 Jul 2020 08:27:30 PM EDT
Built host: basecamp
C bindings: yes
C++ bindings: no
Fort mpif.h: yes (all)
Fort use mpi: yes (full: ignore TKR)
Fort use mpi size: deprecated-ompi-info-value
Fort use mpi_f08: yes
Fort mpi_f08 compliance: The mpi_f08 module is available, but due to
limitations in the
/opt/mpi/gcc-9.3.0/openmpi-
4.0.3/nocuda/bin/mpifort
compiler and/or Open MPI, does not support
the
following: array subsections, direct passthru
(where possible) to underlying Open MPI's C
functionality
Fort mpi_f08 subarrays: no
Java bindings: no
Wrapper compiler rpath: runpath
C compiler: /opt/mpi/gcc-9.3.0/openmpi-
4.0.3/nocuda/bin/mpicc
C compiler absolute:
C compiler family name: GNU
C compiler version: 9.3.0
C++ compiler: /opt/mpi/gcc-9.3.0/openmpi-
4.0.3/nocuda/bin/mpic++
C++ compiler absolute: none
Fort compiler: /opt/mpi/gcc-9.3.0/openmpi-
4.0.3/nocuda/bin/mpifort
Fort compiler abs:
Fort ignore TKR: yes (!GCC$ ATTRIBUTES NO_ARG_CHECK ::)
Fort 08 assumed shape: yes
Fort optional args: yes
Fort INTERFACE: yes
Fort ISO_FORTRAN_ENV: yes
Fort STORAGE_SIZE: yes
Fort BIND(C) (all): yes
Fort ISO_C_BINDING: yes
Fort SUBROUTINE BIND(C): yes
Fort TYPE,BIND(C): yes
Fort T,BIND(C,name='a'): yes
Fort PRIVATE: yes
Fort PROTECTED: yes
Fort ABSTRACT: yes
Fort ASYNCHRONOUS: yes
Fort PROCEDURE: yes
Fort USE...ONLY: yes
Fort C_FUNLOC: yes
Fort f08 using wrappers: yes
Fort MPI_SIZEOF: yes
C profiling: yes
C++ profiling: no
Fort mpif.h profiling: yes
Fort use mpi profiling: yes
Fort use mpi_f08 prof: yes
C++ exceptions: no
Thread support: posix (MPI_THREAD_MULTIPLE: yes, OPAL
support: yes,
OMPI progress: no, ORTE progress: yes, Event
lib:
yes)
Sparse Groups: no
Internal debug support: no
MPI interface warnings: yes
MPI parameter check: runtime
Memory profiling support: no
Memory debugging support: no
dl support: yes
Heterogeneous support: no
mpirun default --prefix: no
MPI_WTIME support: native
Symbol vis. support: yes
Host topology support: yes
IPv6 support: no
MPI1 compatibility: no
MPI extensions: affinity, cuda, pcollreq
FT Checkpoint support: no (checkpoint thread: no)
C/R Enabled Debugging: no
MPI_MAX_PROCESSOR_NAME: 256
MPI_MAX_ERROR_STRING: 256
MPI_MAX_OBJECT_NAME: 64
MPI_MAX_INFO_KEY: 36
MPI_MAX_INFO_VAL: 256
MPI_MAX_PORT_NAME: 1024
MPI_MAX_DATAREP_STRING: 128
MCA allocator: basic (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA allocator: bucket (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA backtrace: execinfo (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA btl: self (MCA v2.1.0, API v3.1.0, Component
v4.0.4)
MCA btl: tcp (MCA v2.1.0, API v3.1.0, Component
v4.0.4)
MCA btl: vader (MCA v2.1.0, API v3.1.0, Component
v4.0.4)
MCA compress: bzip (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA compress: gzip (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA crs: none (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA dl: dlopen (MCA v2.1.0, API v1.0.0, Component
v4.0.4)
MCA event: libevent2022 (MCA v2.1.0, API v2.0.0,
Component
v4.0.4)
MCA hwloc: hwloc201 (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA if: linux_ipv6 (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA if: posix_ipv4 (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA installdirs: env (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA installdirs: config (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA memory: patcher (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA mpool: hugepage (MCA v2.1.0, API v3.0.0, Component
v4.0.4)
MCA patcher: overwrite (MCA v2.1.0, API v1.0.0, Component
v4.0.4)
MCA pmix: pmix3x (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA pmix: isolated (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA pmix: flux (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA pstat: linux (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA rcache: grdma (MCA v2.1.0, API v3.3.0, Component
v4.0.4)
MCA reachable: weighted (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA shmem: sysv (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA shmem: mmap (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA shmem: posix (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA timer: linux (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA errmgr: default_app (MCA v2.1.0, API v3.0.0,
Component
v4.0.4)
MCA errmgr: default_tool (MCA v2.1.0, API v3.0.0,
Component
v4.0.4)
MCA errmgr: default_orted (MCA v2.1.0, API v3.0.0,
Component
v4.0.4)
MCA errmgr: default_hnp (MCA v2.1.0, API v3.0.0,
Component
v4.0.4)
MCA ess: hnp (MCA v2.1.0, API v3.0.0, Component
v4.0.4)
MCA ess: tool (MCA v2.1.0, API v3.0.0, Component
v4.0.4)
MCA ess: env (MCA v2.1.0, API v3.0.0, Component
v4.0.4)
MCA ess: singleton (MCA v2.1.0, API v3.0.0, Component
v4.0.4)
MCA ess: pmi (MCA v2.1.0, API v3.0.0, Component
v4.0.4)
MCA ess: slurm (MCA v2.1.0, API v3.0.0, Component
v4.0.4)
MCA filem: raw (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA grpcomm: direct (MCA v2.1.0, API v3.0.0, Component
v4.0.4)
MCA iof: orted (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA iof: hnp (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA iof: tool (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA odls: pspawn (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA odls: default (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA oob: tcp (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA plm: rsh (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA plm: isolated (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA plm: slurm (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA ras: simulator (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA ras: slurm (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA regx: naive (MCA v2.1.0, API v1.0.0, Component
v4.0.4)
MCA regx: reverse (MCA v2.1.0, API v1.0.0, Component
v4.0.4)
MCA regx: fwd (MCA v2.1.0, API v1.0.0, Component
v4.0.4)
MCA rmaps: mindist (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA rmaps: resilient (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA rmaps: seq (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA rmaps: rank_file (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA rmaps: round_robin (MCA v2.1.0, API v2.0.0,
Component
v4.0.4)
MCA rmaps: ppr (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA rml: oob (MCA v2.1.0, API v3.0.0, Component
v4.0.4)
MCA routed: direct (MCA v2.1.0, API v3.0.0, Component
v4.0.4)
MCA routed: binomial (MCA v2.1.0, API v3.0.0, Component
v4.0.4)
MCA routed: radix (MCA v2.1.0, API v3.0.0, Component
v4.0.4)
MCA rtc: hwloc (MCA v2.1.0, API v1.0.0, Component
v4.0.4)
MCA schizo: orte (MCA v2.1.0, API v1.0.0, Component
v4.0.4)
MCA schizo: ompi (MCA v2.1.0, API v1.0.0, Component
v4.0.4)
MCA schizo: flux (MCA v2.1.0, API v1.0.0, Component
v4.0.4)
MCA schizo: slurm (MCA v2.1.0, API v1.0.0, Component
v4.0.4)
MCA state: tool (MCA v2.1.0, API v1.0.0, Component
v4.0.4)
MCA state: hnp (MCA v2.1.0, API v1.0.0, Component
v4.0.4)
MCA state: orted (MCA v2.1.0, API v1.0.0, Component
v4.0.4)
MCA state: novm (MCA v2.1.0, API v1.0.0, Component
v4.0.4)
MCA state: app (MCA v2.1.0, API v1.0.0, Component
v4.0.4)
MCA bml: r2 (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA coll: tuned (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA coll: sync (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA coll: libnbc (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA coll: monitoring (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA coll: basic (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA coll: inter (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA coll: self (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA coll: sm (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA fbtl: posix (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA fcoll: two_phase (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA fcoll: dynamic (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA fcoll: vulcan (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA fcoll: dynamic_gen2 (MCA v2.1.0, API v2.0.0,
Component
v4.0.4)
MCA fcoll: individual (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA fs: ufs (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA io: ompio (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA io: romio321 (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA osc: monitoring (MCA v2.1.0, API v3.0.0, Component
v4.0.4)
MCA osc: rdma (MCA v2.1.0, API v3.0.0, Component
v4.0.4)
MCA osc: pt2pt (MCA v2.1.0, API v3.0.0, Component
v4.0.4)
MCA osc: sm (MCA v2.1.0, API v3.0.0, Component v4.0.4)
MCA pml: v (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA pml: cm (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA pml: ob1 (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA pml: monitoring (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA rte: orte (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA sharedfp: sm (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA sharedfp: individual (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA sharedfp: lockedfile (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA topo: basic (MCA v2.1.0, API v2.2.0, Component
v4.0.4)
MCA topo: treematch (MCA v2.1.0, API v2.2.0, Component
v4.0.4)
MCA vprotocol: pessimist (MCA v2.1.0, API v2.0.0, Component
v4.0.4)

---

Can anyone guide me in the right direction? Please let me know if you
need additional info. You can also reach me at GitHub, if an issue is
created on visit-users/live-customer-support.

Thanks,
Wileam Y. Phan
PhD student, Dept. of Physics & Astronomy
University of Tennessee, Knoxville
GitHub: @wyphan

$ ./configure --with-szlib=${LIBAEC_DIR} --with-hdf5=${HDF5_DIR}/include,${HDF5_DIR}/lib
--prefix=/opt/hdf5/silo-4.10.2/gcc-9.3.0

Configure Summary
Compiling Options:
C Compiler /usr/bin/gcc
CPPFLAGS -I/opt/hdf5/hdf5-1.12.0/gcc-9.3.0/include
CFLAGS -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -Wdeclaration-after-
statement
LDFLAGS -L/opt/hdf5/hdf5-1.12.0/gcc-9.3.0/lib -L/opt/hdf5/libaec-1.0.4/gcc-9.3.0/lib
-L/opt/hdf5/libaec-1.0.4/gcc-9.3.0/lib
LIBS -lhdf5 -lsz -lsz -lz  -lm -lsz
Languages:
C++ Compiler /usr/bin/g++
CXXFLAGS -fPIC
Fortran Compiler /usr/bin/gfortran
FCFLAGS -g -O2
FCLIBS  -L/opt/openblas/openblas-0.3.10/gcc-9.3.0/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/9
-L/usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-
gnu/9/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu
-L/usr/lib/../lib -L/opt/openblas/openblas-0.3.10/gcc-9.3.0/lib -L/usr/lib/gcc/x86_64-linux-
gnu/9/../../.. -lgfortran -lm -lquadmath
Features:
Browser @UsingBrowser@
Readline @UsingReadline@
HDF5 @UsingHDF5@
Silex @UsingSilex@
Qt @UsingQt@
Qt moc Compiler
Qt CXXFLAGS
Qt LIBS
Python @UsingPython@
Python Compiler
Python CPPFLAGS

$ ./configure --prefix=/opt/hdf5/libaec-1.0.4/gcc-9.3.0

checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking how to print strings... printf
checking for gcc... /usr/bin/gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether /usr/bin/gcc accepts -g... yes
checking for /usr/bin/gcc option to accept ISO C89... none needed
checking whether /usr/bin/gcc understands -c and -o together... yes
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by /usr/bin/gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format...
func_convert_file_noop
checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking for gawk... gawk
checking command to parse /usr/bin/nm -B output from /usr/bin/gcc object... ok
checking for sysroot... no
checking for a working dd... /usr/bin/dd
checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1
checking for mt... mt
checking if mt is a manifest tool... no
checking how to run the C preprocessor... /usr/bin/gcc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h.. truncated...

---

[markcmiller86]

Date: Thu, 17 Dec 2020 16:46:07 -0800
From: notifications at github.com (Wileam Y. Phan)
This post was imported from the visit-users@ornl.gov email archive

---

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---

Hi,

I'm trying to compile SILO 4.10.2 from the tarball downloaded from
https://wci.llnl.gov/simulation/computer-codes/silo/downloads
with the default GCC version (9.3.0) from Ubuntu repositories for
Ubuntu 20.04.1 LTS.

I'm using LibAEC (SZIP replacement) 1.0.4 from
https://gitlab.dkrz.de/k202009/libaec,
and HDF5 1.12.0 (compiled from source, in serial mode).

SILO build crashes with the following error:
'''
silo_hdf5.c: In function ?db_hdf5_process_file_options?:
silo_hdf5.c:4667:2: warning: #warning REMOVED WINDOWS SPECIFIC CHECK [-
Wcpp]
4667 | #warning REMOVED WINDOWS SPECIFIC CHECK
|  ^''''''
silo_hdf5.c:4808:2: warning: #warning REMOVED WINDOWS SPECIFIC CHECK [-
Wcpp]
4808 | #warning REMOVED WINDOWS SPECIFIC CHECK
|  ^''''''
silo_hdf5.c: In function ?db_hdf5_initiate_close?:
silo_hdf5.c:5442:47: warning: format ?%d? expects argument of type
?int?, but argument 4 has type ?hid_t? {aka ?long int?} [-Wformat=]
5442 |                 sprintf(tmp, ' '%.235s ' (id=%d), ', name,
ooids[i]);
|                                              ~^            '''~
'''~
|                                               |
|
|                                               int
hid_t {aka long int}
|                                              %ld
In file included from /opt/hdf5/hdf5-1.12.0/gcc-
9.3.0/include/H5public.h:32,
from /opt/hdf5/hdf5-1.12.0/gcc-
9.3.0/include/hdf5.h:22,
from silo_hdf5_private.h:71,
from silo_hdf5.c:72:
silo_hdf5.c: In function ?db_hdf5_SortObjectsByOffset?:
silo_hdf5.c:15779:18: error: too few arguments to function
?H5Oget_info3?
15779 |                  H5Oget_info(oid, &oinfo)<0 ||
|                  ^'''''''''~
In file included from /opt/hdf5/hdf5-1.12.0/gcc-
9.3.0/include/H5Apublic.h:22,
from /opt/hdf5/hdf5-1.12.0/gcc-
9.3.0/include/hdf5.h:23,
from silo_hdf5_private.h:71,
from silo_hdf5.c:72:
/opt/hdf5/hdf5-1.12.0/gcc-9.3.0/include/H5Opublic.h:187:15: note:
declared here
187 | H5_DLL herr_t H5Oget_info3(hid_t loc_id, H5O_info2_t *oinfo,
unsigned fields);
|               ^'''''''''~~
silo_hdf5.c:15783:38: error: ?H5O_info2_t? {aka ?struct H5O_info2_t?}
has no member named ?addr?
15783 |                 iop[i].offset = oinfo.addr;
|                                      ^
mv -f .deps/H5FDsilo.Tpo .deps/H5FDsilo.Plo
make[4]: *** [Makefile:386: silo_hdf5.lo] Error 1
'''

---

Attached are the config files and build logs for all three libraries.

Some system info:
'''
$ uname -a
Linux basecamp 5.4.0-58-generic #64-Ubuntu SMP Wed Dec 9 08:16:25 UTC
2020 x86_64 x86_64 x86_64 GNU/Linux
'''
'''
$ lsb_release -a
LSB Version:    core-11.1.0ubuntu2-noarch:printing-11.1.0ubuntu2-
noarch:security-11.1.0ubuntu2-noarch
Distributor ID: Ubuntu
Description:    Ubuntu 20.04.1 LTS
Release:        20.04
Codename:       focal
'''
'''
$ ompi_info
Package: Open MPI wyp at basecamp Distribution
Open MPI: 4.0.4
Open MPI repo revision: v4.0.4
Open MPI release date: Jun 10, 2020
Open RTE: 4.0.4
Open RTE repo revision: v4.0.4
Open RTE release date: Jun 10, 2020
OPAL: 4.0.4
OPAL repo revision: v4.0.4
OPAL release date: Jun 10, 2020
MPI API: 3.1.0
Ident string: 4.0.4
Prefix: /opt/mpi/gcc-9.3.0/openmpi-4.0.4/nocuda
Configured architecture: x86_64-unknown-linux-gnu
Configure host: basecamp
Configured by: wyp
Configured on: Fri Jul 17 20:19:52 EDT 2020
Configure host: basecamp
Configure command line: '--prefix=/opt/mpi/gcc-9.3.0/openmpi-
4.0.4/nocuda'
Built by: wyp
Built on: Fri 17 Jul 2020 08:27:30 PM EDT
Built host: basecamp
C bindings: yes
C++ bindings: no
Fort mpif.h: yes (all)
Fort use mpi: yes (full: ignore TKR)
Fort use mpi size: deprecated-ompi-info-value
Fort use mpi_f08: yes
Fort mpi_f08 compliance: The mpi_f08 module is available, but due to
limitations in the
/opt/mpi/gcc-9.3.0/openmpi-
4.0.3/nocuda/bin/mpifort
compiler and/or Open MPI, does not support
the
following: array subsections, direct passthru
(where possible) to underlying Open MPI's C
functionality
Fort mpi_f08 subarrays: no
Java bindings: no
Wrapper compiler rpath: runpath
C compiler: /opt/mpi/gcc-9.3.0/openmpi-
4.0.3/nocuda/bin/mpicc
C compiler absolute:
C compiler family name: GNU
C compiler version: 9.3.0
C++ compiler: /opt/mpi/gcc-9.3.0/openmpi-
4.0.3/nocuda/bin/mpic++
C++ compiler absolute: none
Fort compiler: /opt/mpi/gcc-9.3.0/openmpi-
4.0.3/nocuda/bin/mpifort
Fort compiler abs:
Fort ignore TKR: yes (!GCC$ ATTRIBUTES NO_ARG_CHECK ::)
Fort 08 assumed shape: yes
Fort optional args: yes
Fort INTERFACE: yes
Fort ISO_FORTRAN_ENV: yes
Fort STORAGE_SIZE: yes
Fort BIND(C) (all): yes
Fort ISO_C_BINDING: yes
Fort SUBROUTINE BIND(C): yes
Fort TYPE,BIND(C): yes
Fort T,BIND(C,name='a'): yes
Fort PRIVATE: yes
Fort PROTECTED: yes
Fort ABSTRACT: yes
Fort ASYNCHRONOUS: yes
Fort PROCEDURE: yes
Fort USE...ONLY: yes
Fort C_FUNLOC: yes
Fort f08 using wrappers: yes
Fort MPI_SIZEOF: yes
C profiling: yes
C++ profiling: no
Fort mpif.h profiling: yes
Fort use mpi profiling: yes
Fort use mpi_f08 prof: yes
C++ exceptions: no
Thread support: posix (MPI_THREAD_MULTIPLE: yes, OPAL
support: yes,
OMPI progress: no, ORTE progress: yes, Event
lib:
yes)
Sparse Groups: no
Internal debug support: no
MPI interface warnings: yes
MPI parameter check: runtime
Memory profiling support: no
Memory debugging support: no
dl support: yes
Heterogeneous support: no
mpirun default --prefix: no
MPI_WTIME support: native
Symbol vis. support: yes
Host topology support: yes
IPv6 support: no
MPI1 compatibility: no
MPI extensions: affinity, cuda, pcollreq
FT Checkpoint support: no (checkpoint thread: no)
C/R Enabled Debugging: no
MPI_MAX_PROCESSOR_NAME: 256
MPI_MAX_ERROR_STRING: 256
MPI_MAX_OBJECT_NAME: 64
MPI_MAX_INFO_KEY: 36
MPI_MAX_INFO_VAL: 256
MPI_MAX_PORT_NAME: 1024
MPI_MAX_DATAREP_STRING: 128
MCA allocator: basic (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA allocator: bucket (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA backtrace: execinfo (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA btl: self (MCA v2.1.0, API v3.1.0, Component
v4.0.4)
MCA btl: tcp (MCA v2.1.0, API v3.1.0, Component
v4.0.4)
MCA btl: vader (MCA v2.1.0, API v3.1.0, Component
v4.0.4)
MCA compress: bzip (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA compress: gzip (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA crs: none (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA dl: dlopen (MCA v2.1.0, API v1.0.0, Component
v4.0.4)
MCA event: libevent2022 (MCA v2.1.0, API v2.0.0,
Component
v4.0.4)
MCA hwloc: hwloc201 (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA if: linux_ipv6 (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA if: posix_ipv4 (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA installdirs: env (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA installdirs: config (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA memory: patcher (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA mpool: hugepage (MCA v2.1.0, API v3.0.0, Component
v4.0.4)
MCA patcher: overwrite (MCA v2.1.0, API v1.0.0, Component
v4.0.4)
MCA pmix: pmix3x (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA pmix: isolated (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA pmix: flux (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA pstat: linux (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA rcache: grdma (MCA v2.1.0, API v3.3.0, Component
v4.0.4)
MCA reachable: weighted (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA shmem: sysv (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA shmem: mmap (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA shmem: posix (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA timer: linux (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA errmgr: default_app (MCA v2.1.0, API v3.0.0,
Component
v4.0.4)
MCA errmgr: default_tool (MCA v2.1.0, API v3.0.0,
Component
v4.0.4)
MCA errmgr: default_orted (MCA v2.1.0, API v3.0.0,
Component
v4.0.4)
MCA errmgr: default_hnp (MCA v2.1.0, API v3.0.0,
Component
v4.0.4)
MCA ess: hnp (MCA v2.1.0, API v3.0.0, Component
v4.0.4)
MCA ess: tool (MCA v2.1.0, API v3.0.0, Component
v4.0.4)
MCA ess: env (MCA v2.1.0, API v3.0.0, Component
v4.0.4)
MCA ess: singleton (MCA v2.1.0, API v3.0.0, Component
v4.0.4)
MCA ess: pmi (MCA v2.1.0, API v3.0.0, Component
v4.0.4)
MCA ess: slurm (MCA v2.1.0, API v3.0.0, Component
v4.0.4)
MCA filem: raw (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA grpcomm: direct (MCA v2.1.0, API v3.0.0, Component
v4.0.4)
MCA iof: orted (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA iof: hnp (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA iof: tool (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA odls: pspawn (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA odls: default (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA oob: tcp (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA plm: rsh (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA plm: isolated (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA plm: slurm (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA ras: simulator (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA ras: slurm (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA regx: naive (MCA v2.1.0, API v1.0.0, Component
v4.0.4)
MCA regx: reverse (MCA v2.1.0, API v1.0.0, Component
v4.0.4)
MCA regx: fwd (MCA v2.1.0, API v1.0.0, Component
v4.0.4)
MCA rmaps: mindist (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA rmaps: resilient (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA rmaps: seq (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA rmaps: rank_file (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA rmaps: round_robin (MCA v2.1.0, API v2.0.0,
Component
v4.0.4)
MCA rmaps: ppr (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA rml: oob (MCA v2.1.0, API v3.0.0, Component
v4.0.4)
MCA routed: direct (MCA v2.1.0, API v3.0.0, Component
v4.0.4)
MCA routed: binomial (MCA v2.1.0, API v3.0.0, Component
v4.0.4)
MCA routed: radix (MCA v2.1.0, API v3.0.0, Component
v4.0.4)
MCA rtc: hwloc (MCA v2.1.0, API v1.0.0, Component
v4.0.4)
MCA schizo: orte (MCA v2.1.0, API v1.0.0, Component
v4.0.4)
MCA schizo: ompi (MCA v2.1.0, API v1.0.0, Component
v4.0.4)
MCA schizo: flux (MCA v2.1.0, API v1.0.0, Component
v4.0.4)
MCA schizo: slurm (MCA v2.1.0, API v1.0.0, Component
v4.0.4)
MCA state: tool (MCA v2.1.0, API v1.0.0, Component
v4.0.4)
MCA state: hnp (MCA v2.1.0, API v1.0.0, Component
v4.0.4)
MCA state: orted (MCA v2.1.0, API v1.0.0, Component
v4.0.4)
MCA state: novm (MCA v2.1.0, API v1.0.0, Component
v4.0.4)
MCA state: app (MCA v2.1.0, API v1.0.0, Component
v4.0.4)
MCA bml: r2 (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA coll: tuned (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA coll: sync (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA coll: libnbc (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA coll: monitoring (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA coll: basic (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA coll: inter (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA coll: self (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA coll: sm (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA fbtl: posix (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA fcoll: two_phase (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA fcoll: dynamic (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA fcoll: vulcan (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA fcoll: dynamic_gen2 (MCA v2.1.0, API v2.0.0,
Component
v4.0.4)
MCA fcoll: individual (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA fs: ufs (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA io: ompio (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA io: romio321 (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA osc: monitoring (MCA v2.1.0, API v3.0.0, Component
v4.0.4)
MCA osc: rdma (MCA v2.1.0, API v3.0.0, Component
v4.0.4)
MCA osc: pt2pt (MCA v2.1.0, API v3.0.0, Component
v4.0.4)
MCA osc: sm (MCA v2.1.0, API v3.0.0, Component v4.0.4)
MCA pml: v (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA pml: cm (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA pml: ob1 (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA pml: monitoring (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA rte: orte (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA sharedfp: sm (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA sharedfp: individual (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA sharedfp: lockedfile (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA topo: basic (MCA v2.1.0, API v2.2.0, Component
v4.0.4)
MCA topo: treematch (MCA v2.1.0, API v2.2.0, Component
v4.0.4)
MCA vprotocol: pessimist (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
'''

---

Can anyone guide me in the right direction? Please let me know if you
need additional info.

---

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Reply to this email directly or view it on GitHub:
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users/attachments/20201217/57a2d43a/attachment.htm>

---

[markcmiller86]

Date: Thu, 17 Dec 2020 17:00:46 -0800
From: notifications at github.com (Wileam Y. Phan)
This post was imported from the visit-users@ornl.gov email archive

---

Here are the email attachments.
[hdf5-config-gcc9.3.0.txt](https://github.com/visit-dav/live-customer-
response/files/5712982/hdf5-config-gcc9.3.0.txt)
[libaec-config-gcc9.3.0.txt](https://github.com/visit-dav/live-customer-
response/files/5712983/libaec-config-gcc9.3.0.txt)
[silo-config-gcc9.3.0.txt](https://github.com/visit-dav/live-customer-response/files/5712984/silo-
config-gcc9.3.0.txt)
[hdf5-build-gcc9.3.0.log.gz](https://github.com/visit-dav/live-customer-
response/files/5712985/hdf5-build-gcc9.3.0.log.gz)
[libaec-build-gcc9.3.0.log.gz](https://github.com/visit-dav/live-customer-
response/files/5712986/libaec-build-gcc9.3.0.log.gz)
[silo-build-gcc9.3.0.log.gz](https://github.com/visit-dav/live-customer-response/files/5712987/silo-
build-gcc9.3.0.log.gz)

---

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---

[markcmiller86]

Date: Thu, 17 Dec 2020 23:38:14 -0800
From: cessenat at free.fr (Olivier Cessenat)
This post was imported from the visit-users@ornl.gov email archive

---

Hello Wileam,

I personally compile Silo with hdf5 release 1.8.7, the LLNL build_visit
from VisIt 3.1.4 uses 1.8.14, and I have colleagues who used 1.8.20?
successfully.

Probably your HDF5 too recent release broke it's API for Silo.

Olivier Cessenat.

Le 18/12/2020 ? 01:25, Phan, Wileam via visit-users a ?crit?:
> Hi,
>
> I'm trying to compile SILO 4.10.2 from the tarball downloaded from
> https://wci.llnl.gov/simulation/computer-codes/silo/downloads
> with the default GCC version (9.3.0) from Ubuntu repositories for
> Ubuntu 20.04.1 LTS.
>
> I'm using LibAEC (SZIP replacement) 1.0.4 from
> https://gitlab.dkrz.de/k202009/libaec,
> and HDF5 1.12.0 (compiled from source, in serial mode).
>
> SILO build crashes with the following error:
>
> silo_hdf5.c: In function ?db_hdf5_process_file_options?:
> silo_hdf5.c:4667:2: warning: #warning REMOVED WINDOWS SPECIFIC CHECK [-
> Wcpp]
>   4667 | #warning REMOVED WINDOWS SPECIFIC CHECK
>        |  ^''''''
> silo_hdf5.c:4808:2: warning: #warning REMOVED WINDOWS SPECIFIC CHECK [-
> Wcpp]
>   4808 | #warning REMOVED WINDOWS SPECIFIC CHECK
>        |  ^''''''
> silo_hdf5.c: In function ?db_hdf5_initiate_close?:
> silo_hdf5.c:5442:47: warning: format ?%d? expects argument of type
> ?int?, but argument 4 has type ?hid_t? {aka ?long int?} [-Wformat=]
>   5442 |                 sprintf(tmp, ' '%.235s ' (id=%d), ', name,
> ooids[i]);
>        |                                              ~^            '''~
> '''~
>        |                                               |
>   |
>        |                                               int
>   hid_t {aka long int}
>        |                                              %ld
> In file included from /opt/hdf5/hdf5-1.12.0/gcc-
> 9.3.0/include/H5public.h:32,
>                   from /opt/hdf5/hdf5-1.12.0/gcc-
> 9.3.0/include/hdf5.h:22,
>                   from silo_hdf5_private.h:71,
>                   from silo_hdf5.c:72:
> silo_hdf5.c: In function ?db_hdf5_SortObjectsByOffset?:
> silo_hdf5.c:15779:18: error: too few arguments to function
> ?H5Oget_info3?
> 15779 |                  H5Oget_info(oid, &oinfo)<0 ||
>        |                  ^'''''''''~
> In file included from /opt/hdf5/hdf5-1.12.0/gcc-
> 9.3.0/include/H5Apublic.h:22,
>                   from /opt/hdf5/hdf5-1.12.0/gcc-
> 9.3.0/include/hdf5.h:23,
>                   from silo_hdf5_private.h:71,
>                   from silo_hdf5.c:72:
> /opt/hdf5/hdf5-1.12.0/gcc-9.3.0/include/H5Opublic.h:187:15: note:
> declared here
>    187 | H5_DLL herr_t H5Oget_info3(hid_t loc_id, H5O_info2_t *oinfo,
> unsigned fields);
>        |               ^'''''''''~~
> silo_hdf5.c:15783:38: error: ?H5O_info2_t? {aka ?struct H5O_info2_t?}
> has no member named ?addr?
> 15783 |                 iop[i].offset = oinfo.addr;
>        |                                      ^
> mv -f .deps/H5FDsilo.Tpo .deps/H5FDsilo.Plo
> make[4]: *** [Makefile:386: silo_hdf5.lo] Error 1
>
> ---
>
> Attached are the config files and build logs for all three libraries.
>
> Some system info:
>
> $ uname -a
> Linux basecamp 5.4.0-58-generic #64-Ubuntu SMP Wed Dec 9 08:16:25 UTC
> 2020 x86_64 x86_64 x86_64 GNU/Linux
>
> $ lsb_release -a
> LSB Version:  core-11.1.0ubuntu2-noarch:printing-11.1.0ubuntu2-
> noarch:security-11.1.0ubuntu2-noarch
> Distributor ID:       Ubuntu
> Description:  Ubuntu 20.04.1 LTS
> Release:      20.04
> Codename:     focal
>
> $ ompi_info
>                   Package: Open MPI wyp at basecamp Distribution
>                  Open MPI: 4.0.4
>    Open MPI repo revision: v4.0.4
>     Open MPI release date: Jun 10, 2020
>                  Open RTE: 4.0.4
>    Open RTE repo revision: v4.0.4
>     Open RTE release date: Jun 10, 2020
>                      OPAL: 4.0.4
>        OPAL repo revision: v4.0.4
>         OPAL release date: Jun 10, 2020
>                   MPI API: 3.1.0
>              Ident string: 4.0.4
>                    Prefix: /opt/mpi/gcc-9.3.0/openmpi-4.0.4/nocuda
>   Configured architecture: x86_64-unknown-linux-gnu
>            Configure host: basecamp
>             Configured by: wyp
>             Configured on: Fri Jul 17 20:19:52 EDT 2020
>            Configure host: basecamp
>    Configure command line: '--prefix=/opt/mpi/gcc-9.3.0/openmpi-
> 4.0.4/nocuda'
>                  Built by: wyp
>                  Built on: Fri 17 Jul 2020 08:27:30 PM EDT
>                Built host: basecamp
>                C bindings: yes
>              C++ bindings: no
>               Fort mpif.h: yes (all)
>              Fort use mpi: yes (full: ignore TKR)
>         Fort use mpi size: deprecated-ompi-info-value
>          Fort use mpi_f08: yes
>   Fort mpi_f08 compliance: The mpi_f08 module is available, but due to
>                            limitations in the
>                            /opt/mpi/gcc-9.3.0/openmpi-
> 4.0.3/nocuda/bin/mpifort
>                            compiler and/or Open MPI, does not support
> the
>                            following: array subsections, direct passthru
>                            (where possible) to underlying Open MPI's C
>                            functionality
>    Fort mpi_f08 subarrays: no
>             Java bindings: no
>    Wrapper compiler rpath: runpath
>                C compiler: /opt/mpi/gcc-9.3.0/openmpi-
> 4.0.3/nocuda/bin/mpicc
>       C compiler absolute:
>    C compiler family name: GNU
>        C compiler version: 9.3.0
>              C++ compiler: /opt/mpi/gcc-9.3.0/openmpi-
> 4.0.3/nocuda/bin/mpic++
>     C++ compiler absolute: none
>             Fort compiler: /opt/mpi/gcc-9.3.0/openmpi-
> 4.0.3/nocuda/bin/mpifort
>         Fort compiler abs:
>           Fort ignore TKR: yes (!GCC$ ATTRIBUTES NO_ARG_CHECK ::)
>     Fort 08 assumed shape: yes
>        Fort optional args: yes
>            Fort INTERFACE: yes
>      Fort ISO_FORTRAN_ENV: yes
>         Fort STORAGE_SIZE: yes
>        Fort BIND(C) (all): yes
>        Fort ISO_C_BINDING: yes
>   Fort SUBROUTINE BIND(C): yes
>         Fort TYPE,BIND(C): yes
>   Fort T,BIND(C,name='a'): yes
>              Fort PRIVATE: yes
>            Fort PROTECTED: yes
>             Fort ABSTRACT: yes
>         Fort ASYNCHRONOUS: yes
>            Fort PROCEDURE: yes
>           Fort USE...ONLY: yes
>             Fort C_FUNLOC: yes
>   Fort f08 using wrappers: yes
>           Fort MPI_SIZEOF: yes
>               C profiling: yes
>             C++ profiling: no
>     Fort mpif.h profiling: yes
>    Fort use mpi profiling: yes
>     Fort use mpi_f08 prof: yes
>            C++ exceptions: no
>            Thread support: posix (MPI_THREAD_MULTIPLE: yes, OPAL
> support: yes,
>                            OMPI progress: no, ORTE progress: yes, Event
> lib:
>                            yes)
>             Sparse Groups: no
>    Internal debug support: no
>    MPI interface warnings: yes
>       MPI parameter check: runtime
> Memory profiling support: no
> Memory debugging support: no
>                dl support: yes
>     Heterogeneous support: no
>   mpirun default --prefix: no
>         MPI_WTIME support: native
>       Symbol vis. support: yes
>     Host topology support: yes
>              IPv6 support: no
>        MPI1 compatibility: no
>            MPI extensions: affinity, cuda, pcollreq
>     FT Checkpoint support: no (checkpoint thread: no)
>     C/R Enabled Debugging: no
>    MPI_MAX_PROCESSOR_NAME: 256
>      MPI_MAX_ERROR_STRING: 256
>       MPI_MAX_OBJECT_NAME: 64
>          MPI_MAX_INFO_KEY: 36
>          MPI_MAX_INFO_VAL: 256
>         MPI_MAX_PORT_NAME: 1024
>    MPI_MAX_DATAREP_STRING: 128
>             MCA allocator: basic (MCA v2.1.0, API v2.0.0, Component
> v4.0.4)
>             MCA allocator: bucket (MCA v2.1.0, API v2.0.0, Component
> v4.0.4)
>             MCA backtrace: execinfo (MCA v2.1.0, API v2.0.0, Component
> v4.0.4)
>                   MCA btl: self (MCA v2.1.0, API v3.1.0, Component
> v4.0.4)
>                   MCA btl: tcp (MCA v2.1.0, API v3.1.0, Component
> v4.0.4)
>                   MCA btl: vader (MCA v2.1.0, API v3.1.0, Component
> v4.0.4)
>              MCA compress: bzip (MCA v2.1.0, API v2.0.0, Component
> v4.0.4)
>              MCA compress: gzip (MCA v2.1.0, API v2.0.0, Component
> v4.0.4)
>                   MCA crs: none (MCA v2.1.0, API v2.0.0, Component
> v4.0.4)
>                    MCA dl: dlopen (MCA v2.1.0, API v1.0.0, Component
> v4.0.4)
>                 MCA event: libevent2022 (MCA v2.1.0, API v2.0.0,
> Component
>                            v4.0.4)
>                 MCA hwloc: hwloc201 (MCA v2.1.0, API v2.0.0, Component
> v4.0.4)
>                    MCA if: linux_ipv6 (MCA v2.1.0, API v2.0.0, Component
>                            v4.0.4)
>                    MCA if: posix_ipv4 (MCA v2.1.0, API v2.0.0, Component
>                            v4.0.4)
>           MCA installdirs: env (MCA v2.1.0, API v2.0.0, Component
> v4.0.4)
>           MCA installdirs: config (MCA v2.1.0, API v2.0.0, Component
> v4.0.4)
>                MCA memory: patcher (MCA v2.1.0, API v2.0.0, Component
> v4.0.4)
>                 MCA mpool: hugepage (MCA v2.1.0, API v3.0.0, Component
> v4.0.4)
>               MCA patcher: overwrite (MCA v2.1.0, API v1.0.0, Component
>                            v4.0.4)
>                  MCA pmix: pmix3x (MCA v2.1.0, API v2.0.0, Component
> v4.0.4)
>                  MCA pmix: isolated (MCA v2.1.0, API v2.0.0, Component
> v4.0.4)
>                  MCA pmix: flux (MCA v2.1.0, API v2.0.0, Component
> v4.0.4)
>                 MCA pstat: linux (MCA v2.1.0, API v2.0.0, Component
> v4.0.4)
>                MCA rcache: grdma (MCA v2.1.0, API v3.3.0, Component
> v4.0.4)
>             MCA reachable: weighted (MCA v2.1.0, API v2.0.0, Component
> v4.0.4)
>                 MCA shmem: sysv (MCA v2.1.0, API v2.0.0, Component
> v4.0.4)
>                 MCA shmem: mmap (MCA v2.1.0, API v2.0.0, Component
> v4.0.4)
>                 MCA shmem: posix (MCA v2.1.0, API v2.0.0, Component
> v4.0.4)
>                 MCA timer: linux (MCA v2.1.0, API v2.0.0, Component
> v4.0.4)
>                MCA errmgr: default_app (MCA v2.1.0, API v3.0.0,
> Component
>                            v4.0.4)
>                MCA errmgr: default_tool (MCA v2.1.0, API v3.0.0,
> Component
>                            v4.0.4)
>                MCA errmgr: default_orted (MCA v2.1.0, API v3.0.0,
> Component
>                            v4.0.4)
>                MCA errmgr: default_hnp (MCA v2.1.0, API v3.0.0,
> Component
>                            v4.0.4)
>                   MCA ess: hnp (MCA v2.1.0, API v3.0.0, Component
> v4.0.4)
>                   MCA ess: tool (MCA v2.1.0, API v3.0.0, Component
> v4.0.4)
>                   MCA ess: env (MCA v2.1.0, API v3.0.0, Component
> v4.0.4)
>                   MCA ess: singleton (MCA v2.1.0, API v3.0.0, Component
>                            v4.0.4)
>                   MCA ess: pmi (MCA v2.1.0, API v3.0.0, Component
> v4.0.4)
>                   MCA ess: slurm (MCA v2.1.0, API v3.0.0, Component
> v4.0.4)
>                 MCA filem: raw (MCA v2.1.0, API v2.0.0, Component
> v4.0.4)
>               MCA grpcomm: direct (MCA v2.1.0, API v3.0.0, Component
> v4.0.4)
>                   MCA iof: orted (MCA v2.1.0, API v2.0.0, Component
> v4.0.4)
>                   MCA iof: hnp (MCA v2.1.0, API v2.0.0, Component
> v4.0.4)
>                   MCA iof: tool (MCA v2.1.0, API v2.0.0, Component
> v4.0.4)
>                  MCA odls: pspawn (MCA v2.1.0, API v2.0.0, Component
> v4.0.4)
>                  MCA odls: default (MCA v2.1.0, API v2.0.0, Component
> v4.0.4)
>                   MCA oob: tcp (MCA v2.1.0, API v2.0.0, Component
> v4.0.4)
>                   MCA plm: rsh (MCA v2.1.0, API v2.0.0, Component
> v4.0.4)
>                   MCA plm: isolated (MCA v2.1.0, API v2.0.0, Component
> v4.0.4)
>                   MCA plm: slurm (MCA v2.1.0, API v2.0.0, Component
> v4.0.4)
>                   MCA ras: simulator (MCA v2.1.0, API v2.0.0, Component
>                            v4.0.4)
>                   MCA ras: slurm (MCA v2.1.0, API v2.0.0, Component
> v4.0.4)
>                  MCA regx: naive (MCA v2.1.0, API v1.0.0, Component
> v4.0.4)
>                  MCA regx: reverse (MCA v2.1.0, API v1.0.0, Component
> v4.0.4)
>                  MCA regx: fwd (MCA v2.1.0, API v1.0.0, Component
> v4.0.4)
>                 MCA rmaps: mindist (MCA v2.1.0, API v2.0.0, Component
> v4.0.4)
>                 MCA rmaps: resilient (MCA v2.1.0, API v2.0.0, Component
>                            v4.0.4)
>                 MCA rmaps: seq (MCA v2.1.0, API v2.0.0, Component
> v4.0.4)
>                 MCA rmaps: rank_file (MCA v2.1.0, API v2.0.0, Component
>                            v4.0.4)
>                 MCA rmaps: round_robin (MCA v2.1.0, API v2.0.0,
> Component
>                            v4.0.4)
>                 MCA rmaps: ppr (MCA v2.1.0, API v2.0.0, Component
> v4.0.4)
>                   MCA rml: oob (MCA v2.1.0, API v3.0.0, Component
> v4.0.4)
>                MCA routed: direct (MCA v2.1.0, API v3.0.0, Component
> v4.0.4)
>                MCA routed: binomial (MCA v2.1.0, API v3.0.0, Component
> v4.0.4)
>                MCA routed: radix (MCA v2.1.0, API v3.0.0, Component
> v4.0.4)
>                   MCA rtc: hwloc (MCA v2.1.0, API v1.0.0, Component
> v4.0.4)
>                MCA schizo: orte (MCA v2.1.0, API v1.0.0, Component
> v4.0.4)
>                MCA schizo: ompi (MCA v2.1.0, API v1.0.0, Component
> v4.0.4)
>                MCA schizo: flux (MCA v2.1.0, API v1.0.0, Component
> v4.0.4)
>                MCA schizo: slurm (MCA v2.1.0, API v1.0.0, Component
> v4.0.4)
>                 MCA state: tool (MCA v2.1.0, API v1.0.0, Component
> v4.0.4)
>                 MCA state: hnp (MCA v2.1.0, API v1.0.0, Component
> v4.0.4)
>                 MCA state: orted (MCA v2.1.0, API v1.0.0, Component
> v4.0.4)
>                 MCA state: novm (MCA v2.1.0, API v1.0.0, Component
> v4.0.4)
>                 MCA state: app (MCA v2.1.0, API v1.0.0, Component
> v4.0.4)
>                   MCA bml: r2 (MCA v2.1.0, API v2.0.0, Component v4.0.4)
>                  MCA coll: tuned (MCA v2.1.0, API v2.0.0, Component
> v4.0.4)
>                  MCA coll: sync (MCA v2.1.0, API v2.0.0, Component
> v4.0.4)
>                  MCA coll: libnbc (MCA v2.1.0, API v2.0.0, Component
> v4.0.4)
>                  MCA coll: monitoring (MCA v2.1.0, API v2.0.0, Component
>                            v4.0.4)
>                  MCA coll: basic (MCA v2.1.0, API v2.0.0, Component
> v4.0.4)
>                  MCA coll: inter (MCA v2.1.0, API v2.0.0, Component
> v4.0.4)
>                  MCA coll: self (MCA v2.1.0, API v2.0.0, Component
> v4.0.4)
>                  MCA coll: sm (MCA v2.1.0, API v2.0.0, Component v4.0.4)
>                  MCA fbtl: posix (MCA v2.1.0, API v2.0.0, Component
> v4.0.4)
>                 MCA fcoll: two_phase (MCA v2.1.0, API v2.0.0, Component
>                            v4.0.4)
>                 MCA fcoll: dynamic (MCA v2.1.0, API v2.0.0, Component
> v4.0.4)
>                 MCA fcoll: vulcan (MCA v2.1.0, API v2.0.0, Component
> v4.0.4)
>                 MCA fcoll: dynamic_gen2 (MCA v2.1.0, API v2.0.0,
> Component
>                            v4.0.4)
>                 MCA fcoll: individual (MCA v2.1.0, API v2.0.0, Component
>                            v4.0.4)
>                    MCA fs: ufs (MCA v2.1.0, API v2.0.0, Component
> v4.0.4)
>                    MCA io: ompio (MCA v2.1.0, API v2.0.0, Component
> v4.0.4)
>                    MCA io: romio321 (MCA v2.1.0, API v2.0.0, Component
> v4.0.4)
>                   MCA osc: monitoring (MCA v2.1.0, API v3.0.0, Component
>                            v4.0.4)
>                   MCA osc: rdma (MCA v2.1.0, API v3.0.0, Component
> v4.0.4)
>                   MCA osc: pt2pt (MCA v2.1.0, API v3.0.0, Component
> v4.0.4)
>                   MCA osc: sm (MCA v2.1.0, API v3.0.0, Component v4.0.4)
>                   MCA pml: v (MCA v2.1.0, API v2.0.0, Component v4.0.4)
>                   MCA pml: cm (MCA v2.1.0, API v2.0.0, Component v4.0.4)
>                   MCA pml: ob1 (MCA v2.1.0, API v2.0.0, Component
> v4.0.4)
>                   MCA pml: monitoring (MCA v2.1.0, API v2.0.0, Component
>                            v4.0.4)
>                   MCA rte: orte (MCA v2.1.0, API v2.0.0, Component
> v4.0.4)
>              MCA sharedfp: sm (MCA v2.1.0, API v2.0.0, Component v4.0.4)
>              MCA sharedfp: individual (MCA v2.1.0, API v2.0.0, Component
>                            v4.0.4)
>              MCA sharedfp: lockedfile (MCA v2.1.0, API v2.0.0, Component
>                            v4.0.4)
>                  MCA topo: basic (MCA v2.1.0, API v2.2.0, Component
> v4.0.4)
>                  MCA topo: treematch (MCA v2.1.0, API v2.2.0, Component
>                            v4.0.4)
>             MCA vprotocol: pessimist (MCA v2.1.0, API v2.0.0, Component
>                            v4.0.4)
>
> ---
>
> Can anyone guide me in the right direction? Please let me know if you
> need additional info. You can also reach me at GitHub, if an issue is
> created on visit-users/live-customer-support.
>
> Thanks,
> Wileam Y. Phan
> PhD student, Dept. of Physics & Astronomy
> University of Tennessee, Knoxville
> GitHub: @wyphan
>
> --

> Frequently Asked Questions for VisIt: https://wci.llnl.gov/simulation/computer-
codes/visit/FAQ.html

URL: <https://elist.ornl.gov/mailman/private/visit-
users/attachments/20201218/35784d3a/attachment.htm>

---

[markcmiller86]

Date: Fri, 18 Dec 2020 01:04:35 -0800
From: notifications at github.com (Mark C. Miller)
This post was imported from the visit-users@ornl.gov email archive

---

It looks like [`H5Oget_info`](https://portal.hdfgroup.org/display/HDF5/H5O_GET_INFO) was introduced
to HDF5 in version 1.8. However the overwhelming majority of Silo uses HDF5's 1.6 API and,
therefore, defines the `H5_USE_16_API` symbol to indicate that for HDF5 headers when compiling. But,
since `H5Oget_info` was introduced in 1.8, it has no 1.6 mapping and therefore defaults to whatever
the *default* API of HDF5 installation is...in your case that is 1.12 and the interface to
H5Oget_info has changed. The solution is to *force* the mapping for that symbol to the 1.8 variant
calling `H5Oget_info1(...)` (e.g. add a `1` to the name) and to *force* the mapping of `H5O_info_t`
to `H5O_info1_t` (e.g. add a `1` to the name).

@qkoziol ... shouldn't `#define H5_USE_16_API` funcs added to lib *after* 1.6 to their *lowest* API
as well?

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users/attachments/20201218/f35038bc/attachment.htm>

---

[markcmiller86]

Date: Fri, 18 Dec 2020 01:06:49 -0800
From: notifications at github.com (Mark C. Miller)
This post was imported from the visit-users@ornl.gov email archive

---

I really should upgrade Silo to newer HDF5 API too.

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---

[markcmiller86]

Date: Fri, 18 Dec 2020 01:16:06 -0800
From: miller86 at llnl.gov (Miller, Mark C.)
This post was imported from the visit-users@ornl.gov email archive

---

Hello,

We moved your issue to a GitHub issue in the VisIt project and then I moved it from there to the
Silo issue tracker...

https://github.com/markcmiller86/silo-issues/issues/211

Be sure to have a look at this comment...

https://github.com/markcmiller86/silo-issues/issues/211#issuecomment-747959053

Mark

'Phan, Wileam via visit-users' wrote:

Hi,

I'm trying to compile SILO 4.10.2 from the tarball downloaded from
https://wci.llnl.gov/simulation/computer-codes/silo/downloads
with the default GCC version (9.3.0) from Ubuntu repositories for
Ubuntu 20.04.1 LTS.

I'm using LibAEC (SZIP replacement) 1.0.4 from
https://gitlab.dkrz.de/k202009/libaec,
and HDF5 1.12.0 (compiled from source, in serial mode).

SILO build crashes with the following error:

silo_hdf5.c: In function ?db_hdf5_process_file_options?:
silo_hdf5.c:4667:2: warning: #warning REMOVED WINDOWS SPECIFIC CHECK [-
Wcpp]
4667 | #warning REMOVED WINDOWS SPECIFIC CHECK
|  ^''''''
silo_hdf5.c:4808:2: warning: #warning REMOVED WINDOWS SPECIFIC CHECK [-
Wcpp]
4808 | #warning REMOVED WINDOWS SPECIFIC CHECK
|  ^''''''
silo_hdf5.c: In function ?db_hdf5_initiate_close?:
silo_hdf5.c:5442:47: warning: format ?%d? expects argument of type
?int?, but argument 4 has type ?hid_t? {aka ?long int?} [-Wformat=]
5442 |                 sprintf(tmp, ' '%.235s ' (id=%d), ', name,
ooids[i]);
|                                              ~^            '''~
'''~
|                                               |
|
|                                               int
hid_t {aka long int}
|                                              %ld
In file included from /opt/hdf5/hdf5-1.12.0/gcc-
9.3.0/include/H5public.h:32,
from /opt/hdf5/hdf5-1.12.0/gcc-
9.3.0/include/hdf5.h:22,
from silo_hdf5_private.h:71,
from silo_hdf5.c:72:
silo_hdf5.c: In function ?db_hdf5_SortObjectsByOffset?:
silo_hdf5.c:15779:18: error: too few arguments to function
?H5Oget_info3?
15779 |                  H5Oget_info(oid, &oinfo)<0 ||
|                  ^'''''''''~
In file included from /opt/hdf5/hdf5-1.12.0/gcc-
9.3.0/include/H5Apublic.h:22,
from /opt/hdf5/hdf5-1.12.0/gcc-
9.3.0/include/hdf5.h:23,
from silo_hdf5_private.h:71,
from silo_hdf5.c:72:
/opt/hdf5/hdf5-1.12.0/gcc-9.3.0/include/H5Opublic.h:187:15: note:
declared here
187 | H5_DLL herr_t H5Oget_info3(hid_t loc_id, H5O_info2_t *oinfo,
unsigned fields);
|               ^'''''''''~~
silo_hdf5.c:15783:38: error: ?H5O_info2_t? {aka ?struct H5O_info2_t?}
has no member named ?addr?
15783 |                 iop[i].offset = oinfo.addr;
|                                      ^
mv -f .deps/H5FDsilo.Tpo .deps/H5FDsilo.Plo
make[4]: *** [Makefile:386: silo_hdf5.lo] Error 1

---

Attached are the config files and build logs for all three libraries.

Some system info:

$ uname -a
Linux basecamp 5.4.0-58-generic #64-Ubuntu SMP Wed Dec 9 08:16:25 UTC
2020 x86_64 x86_64 x86_64 GNU/Linux

$ lsb_release -a
LSB Version:       core-11.1.0ubuntu2-noarch:printing-11.1.0ubuntu2-
noarch:security-11.1.0ubuntu2-noarch
Distributor ID:    Ubuntu
Description:        Ubuntu 20.04.1 LTS
Release:               20.04
Codename:         focal

$ ompi_info
Package: Open MPI wyp at basecamp Distribution
Open MPI: 4.0.4
Open MPI repo revision: v4.0.4
Open MPI release date: Jun 10, 2020
Open RTE: 4.0.4
Open RTE repo revision: v4.0.4
Open RTE release date: Jun 10, 2020
OPAL: 4.0.4
OPAL repo revision: v4.0.4
OPAL release date: Jun 10, 2020
MPI API: 3.1.0
Ident string: 4.0.4
Prefix: /opt/mpi/gcc-9.3.0/openmpi-4.0.4/nocuda
Configured architecture: x86_64-unknown-linux-gnu
Configure host: basecamp
Configured by: wyp
Configured on: Fri Jul 17 20:19:52 EDT 2020
Configure host: basecamp
Configure command line: '--prefix=/opt/mpi/gcc-9.3.0/openmpi-
4.0.4/nocuda'
Built by: wyp
Built on: Fri 17 Jul 2020 08:27:30 PM EDT
Built host: basecamp
C bindings: yes
C++ bindings: no
Fort mpif.h: yes (all)
Fort use mpi: yes (full: ignore TKR)
Fort use mpi size: deprecated-ompi-info-value
Fort use mpi_f08: yes
Fort mpi_f08 compliance: The mpi_f08 module is available, but due to
limitations in the
/opt/mpi/gcc-9.3.0/openmpi-
4.0.3/nocuda/bin/mpifort
compiler and/or Open MPI, does not support
the
following: array subsections, direct passthru
(where possible) to underlying Open MPI's C
functionality
Fort mpi_f08 subarrays: no
Java bindings: no
Wrapper compiler rpath: runpath
C compiler: /opt/mpi/gcc-9.3.0/openmpi-
4.0.3/nocuda/bin/mpicc
C compiler absolute:
C compiler family name: GNU
C compiler version: 9.3.0
C++ compiler: /opt/mpi/gcc-9.3.0/openmpi-
4.0.3/nocuda/bin/mpic++
C++ compiler absolute: none
Fort compiler: /opt/mpi/gcc-9.3.0/openmpi-
4.0.3/nocuda/bin/mpifort
Fort compiler abs:
Fort ignore TKR: yes (!GCC$ ATTRIBUTES NO_ARG_CHECK ::)
Fort 08 assumed shape: yes
Fort optional args: yes
Fort INTERFACE: yes
Fort ISO_FORTRAN_ENV: yes
Fort STORAGE_SIZE: yes
Fort BIND(C) (all): yes
Fort ISO_C_BINDING: yes
Fort SUBROUTINE BIND(C): yes
Fort TYPE,BIND(C): yes
Fort T,BIND(C,name='a'): yes
Fort PRIVATE: yes
Fort PROTECTED: yes
Fort ABSTRACT: yes
Fort ASYNCHRONOUS: yes
Fort PROCEDURE: yes
Fort USE...ONLY: yes
Fort C_FUNLOC: yes
Fort f08 using wrappers: yes
Fort MPI_SIZEOF: yes
C profiling: yes
C++ profiling: no
Fort mpif.h profiling: yes
Fort use mpi profiling: yes
Fort use mpi_f08 prof: yes
C++ exceptions: no
Thread support: posix (MPI_THREAD_MULTIPLE: yes, OPAL
support: yes,
OMPI progress: no, ORTE progress: yes, Event
lib:
yes)
Sparse Groups: no
Internal debug support: no
MPI interface warnings: yes
MPI parameter check: runtime
Memory profiling support: no
Memory debugging support: no
dl support: yes
Heterogeneous support: no
mpirun default --prefix: no
MPI_WTIME support: native
Symbol vis. support: yes
Host topology support: yes
IPv6 support: no
MPI1 compatibility: no
MPI extensions: affinity, cuda, pcollreq
FT Checkpoint support: no (checkpoint thread: no)
C/R Enabled Debugging: no
MPI_MAX_PROCESSOR_NAME: 256
MPI_MAX_ERROR_STRING: 256
MPI_MAX_OBJECT_NAME: 64
MPI_MAX_INFO_KEY: 36
MPI_MAX_INFO_VAL: 256
MPI_MAX_PORT_NAME: 1024
MPI_MAX_DATAREP_STRING: 128
MCA allocator: basic (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA allocator: bucket (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA backtrace: execinfo (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA btl: self (MCA v2.1.0, API v3.1.0, Component
v4.0.4)
MCA btl: tcp (MCA v2.1.0, API v3.1.0, Component
v4.0.4)
MCA btl: vader (MCA v2.1.0, API v3.1.0, Component
v4.0.4)
MCA compress: bzip (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA compress: gzip (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA crs: none (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA dl: dlopen (MCA v2.1.0, API v1.0.0, Component
v4.0.4)
MCA event: libevent2022 (MCA v2.1.0, API v2.0.0,
Component
v4.0.4)
MCA hwloc: hwloc201 (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA if: linux_ipv6 (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA if: posix_ipv4 (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA installdirs: env (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA installdirs: config (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA memory: patcher (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA mpool: hugepage (MCA v2.1.0, API v3.0.0, Component
v4.0.4)
MCA patcher: overwrite (MCA v2.1.0, API v1.0.0, Component
v4.0.4)
MCA pmix: pmix3x (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA pmix: isolated (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA pmix: flux (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA pstat: linux (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA rcache: grdma (MCA v2.1.0, API v3.3.0, Component
v4.0.4)
MCA reachable: weighted (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA shmem: sysv (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA shmem: mmap (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA shmem: posix (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA timer: linux (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA errmgr: default_app (MCA v2.1.0, API v3.0.0,
Component
v4.0.4)
MCA errmgr: default_tool (MCA v2.1.0, API v3.0.0,
Component
v4.0.4)
MCA errmgr: default_orted (MCA v2.1.0, API v3.0.0,
Component
v4.0.4)
MCA errmgr: default_hnp (MCA v2.1.0, API v3.0.0,
Component
v4.0.4)
MCA ess: hnp (MCA v2.1.0, API v3.0.0, Component
v4.0.4)
MCA ess: tool (MCA v2.1.0, API v3.0.0, Component
v4.0.4)
MCA ess: env (MCA v2.1.0, API v3.0.0, Component
v4.0.4)
MCA ess: singleton (MCA v2.1.0, API v3.0.0, Component
v4.0.4)
MCA ess: pmi (MCA v2.1.0, API v3.0.0, Component
v4.0.4)
MCA ess: slurm (MCA v2.1.0, API v3.0.0, Component
v4.0.4)
MCA filem: raw (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA grpcomm: direct (MCA v2.1.0, API v3.0.0, Component
v4.0.4)
MCA iof: orted (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA iof: hnp (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA iof: tool (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA odls: pspawn (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA odls: default (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA oob: tcp (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA plm: rsh (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA plm: isolated (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA plm: slurm (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA ras: simulator (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA ras: slurm (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA regx: naive (MCA v2.1.0, API v1.0.0, Component
v4.0.4)
MCA regx: reverse (MCA v2.1.0, API v1.0.0, Component
v4.0.4)
MCA regx: fwd (MCA v2.1.0, API v1.0.0, Component
v4.0.4)
MCA rmaps: mindist (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA rmaps: resilient (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA rmaps: seq (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA rmaps: rank_file (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA rmaps: round_robin (MCA v2.1.0, API v2.0.0,
Component
v4.0.4)
MCA rmaps: ppr (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA rml: oob (MCA v2.1.0, API v3.0.0, Component
v4.0.4)
MCA routed: direct (MCA v2.1.0, API v3.0.0, Component
v4.0.4)
MCA routed: binomial (MCA v2.1.0, API v3.0.0, Component
v4.0.4)
MCA routed: radix (MCA v2.1.0, API v3.0.0, Component
v4.0.4)
MCA rtc: hwloc (MCA v2.1.0, API v1.0.0, Component
v4.0.4)
MCA schizo: orte (MCA v2.1.0, API v1.0.0, Component
v4.0.4)
MCA schizo: ompi (MCA v2.1.0, API v1.0.0, Component
v4.0.4)
MCA schizo: flux (MCA v2.1.0, API v1.0.0, Component
v4.0.4)
MCA schizo: slurm (MCA v2.1.0, API v1.0.0, Component
v4.0.4)
MCA state: tool (MCA v2.1.0, API v1.0.0, Component
v4.0.4)
MCA state: hnp (MCA v2.1.0, API v1.0.0, Component
v4.0.4)
MCA state: orted (MCA v2.1.0, API v1.0.0, Component
v4.0.4)
MCA state: novm (MCA v2.1.0, API v1.0.0, Component
v4.0.4)
MCA state: app (MCA v2.1.0, API v1.0.0, Component
v4.0.4)
MCA bml: r2 (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA coll: tuned (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA coll: sync (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA coll: libnbc (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA coll: monitoring (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA coll: basic (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA coll: inter (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA coll: self (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA coll: sm (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA fbtl: posix (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA fcoll: two_phase (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA fcoll: dynamic (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA fcoll: vulcan (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA fcoll: dynamic_gen2 (MCA v2.1.0, API v2.0.0,
Component
v4.0.4)
MCA fcoll: individual (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA fs: ufs (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA io: ompio (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA io: romio321 (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA osc: monitoring (MCA v2.1.0, API v3.0.0, Component
v4.0.4)
MCA osc: rdma (MCA v2.1.0, API v3.0.0, Component
v4.0.4)
MCA osc: pt2pt (MCA v2.1.0, API v3.0.0, Component
v4.0.4)
MCA osc: sm (MCA v2.1.0, API v3.0.0, Component v4.0.4)
MCA pml: v (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA pml: cm (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA pml: ob1 (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA pml: monitoring (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA rte: orte (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA sharedfp: sm (MCA v2.1.0, API v2.0.0, Component v4.0.4)
MCA sharedfp: individual (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA sharedfp: lockedfile (MCA v2.1.0, API v2.0.0, Component
v4.0.4)
MCA topo: basic (MCA v2.1.0, API v2.2.0, Component
v4.0.4)
MCA topo: treematch (MCA v2.1.0, API v2.2.0, Component
v4.0.4)
MCA vprotocol: pessimist (MCA v2.1.0, API v2.0.0, Component
v4.0.4)

---

Can anyone guide me in the right direction? Please let me know if you
need additional info. You can also reach me at GitHub, if an issue is
created on visit-users/live-customer-support.

Thanks,
Wileam Y. Phan
PhD student, Dept. of Physics & Astronomy
University of Tennessee, Knoxville
GitHub: @wyphan

URL: <https://elist.ornl.gov/mailman/private/visit-
users/attachments/20201218/007ea63e/attachment.htm>

---

[markcmiller86]

Date: Fri, 18 Dec 2020 01:18:28 -0800
From: miller86 at llnl.gov (Miller, Mark C.)
This post was imported from the visit-users@ornl.gov email archive

---

Yes, thanks Olivier. That is basically right.

Though I am pretty hopeful the one change I suggested should fix the compilation issue for 1.12.

Mark

'Olivier Cessenat via visit-users' wrote:

Probably your HDF5 too recent release broke it's API for Silo.

URL: <https://elist.ornl.gov/mailman/private/visit-
users/attachments/20201218/de9ab2b1/attachment.htm>

---

[markcmiller86]

Date: Fri, 18 Dec 2020 14:05:14 -0800
From: vaf0001 at uah.edu (Vladimir Florinski)
This post was imported from the visit-users@ornl.gov email archive

---

I am using HDF 1.10.6, and SILO compiles just fine.

On Fri, Dec 18, 2020 at 3:04 AM Mark C. Miller via visit-users <
visit-users at elist.ornl.gov> wrote:

> It looks like H5Oget_info
> <https://portal.hdfgroup.org/display/HDF5/H5O_GET_INFO> was introduced to
> HDF5 in version 1.8. However the overwhelming majority of Silo uses HDF5's
> 1.6 API and, therefore, defines the H5_USE_16_API symbol to indicate that
> for HDF5 headers when compiling. But, since H5Oget_info was introduced in
> 1.8, it has no 1.6 mapping and therefore defaults to whatever the
> *default* API of HDF5 installation is...in your case that is 1.12 and the
> interface to H5Oget_info has changed. The solution is to *force* the
> mapping for that symbol to the 1.8 variant calling H5Oget_info1(...)
> (e.g. add a 1 to the name) and to *force* the mapping of H5O_info_t to
> H5O_info1_t (e.g. add a 1 to the name).
>
> @qkoziol <https://github.com/qkoziol> ... shouldn't #define H5_USE_16_API
> funcs added to lib *after* 1.6 to their *lowest* API as well?
>
> ?
> You are receiving this because you are subscribed to this thread.
> Reply to this email directly, view it on GitHub
> <https://github.com/visit-dav/live-customer-response/issues/199#issuecomment-747959053>,
> or unsubscribe
> <https://github.com/notifications/unsubscribe-auth/AOLAYZH7VBZONZJJXW6AJZDSVMLKHANCNFSM4VAOY7OQ>
> .
> --

> Frequently Asked Questions for VisIt:
> https://wci.llnl.gov/simulation/computer-codes/visit/FAQ.html

>

---

Vladimir Florinski

URL: <https://elist.ornl.gov/mailman/private/visit-
users/attachments/20201218/f1fb4728/attachment.htm>

---

[markcmiller86]

Date: Fri, 18 Dec 2020 14:07:35 -0800
From: wphan at vols.utk.edu (Phan, Wileam)
This post was imported from the visit-users@ornl.gov email archive

---

Most likely, 1.12.0 breaks SILO because it removes older symbols.

On Fri, Dec 18, 2020, 17:05 Vladimir Florinski via visit-users <
visit-users at elist.ornl.gov> wrote:

> I am using HDF 1.10.6, and SILO compiles just fine.
>
> On Fri, Dec 18, 2020 at 3:04 AM Mark C. Miller via visit-users <
> visit-users at elist.ornl.gov> wrote:
>
>> It looks like H5Oget_info
>> <https://portal.hdfgroup.org/display/HDF5/H5O_GET_INFO> was introduced
>> to HDF5 in version 1.8. However the overwhelming majority of Silo uses
>> HDF5's 1.6 API and, therefore, defines the H5_USE_16_API symbol to
>> indicate that for HDF5 headers when compiling. But, since H5Oget_info
>> was introduced in 1.8, it has no 1.6 mapping and therefore defaults to
>> whatever the *default* API of HDF5 installation is...in your case that
>> is 1.12 and the interface to H5Oget_info has changed. The solution is to
>> *force* the mapping for that symbol to the 1.8 variant calling
>> H5Oget_info1(...) (e.g. add a 1 to the name) and to *force* the mapping
>> of H5O_info_t to H5O_info1_t (e.g. add a 1 to the name).
>>
>> @qkoziol <https://github.com/qkoziol> ... shouldn't #define H5_USE_16_API
>> funcs added to lib *after* 1.6 to their *lowest* API as well?
>>
>> ?
>> You are receiving this because you are subscribed to this thread.
>> Reply to this email directly, view it on GitHub
>> <https://github.com/visit-dav/live-customer-response/issues/199#issuecomment-747959053>,
>> or unsubscribe
>> <https://github.com/notifications/unsubscribe-auth/AOLAYZH7VBZONZJJXW6AJZDSVMLKHANCNFSM4VAOY7OQ>
>> .
>> --

>> Frequently Asked Questions for VisIt:
>> https://wci.llnl.gov/simulation/computer-codes/visit/FAQ.html

>>
>
>
> --
> Vladimir Florinski
> --

> Frequently Asked Questions for VisIt:
> https://wci.llnl.gov/simulation/computer-codes/visit/FAQ.html

URL: <https://elist.ornl.gov/mailman/private/visit-
users/attachments/20201218/7ec351d5/attachment.htm>

---