[Flash-X-users] Getting Flash-X to work
kiyarash Taghiniyarami
kiyarash.niyarami at gmail.com
Fri Aug 30 01:30:58 CDT 2024
Dear Ryan,
I use the HDF5 version of 1.14.3. Its config file is attached.
Best,
Kiya
On Fri, Aug 30, 2024 at 7:19 AM Ryan Farber <rjfarber at umich.edu> wrote:
> Hi Peter,
>
> Thanks for attaching the file. As you can see, the files are sorted
> alphabetically. I don't see any wl* files in your object directory,
> suggesting there is in fact an issue.
>
> Anyway, I am also running into some trouble getting Flash-X up and running
> on my virtual private server.
> Specifically, I have an HDF5 error:
>
> " ../..//Modules/Library/SubcellReconstructionModule.F90 -o
> SubcellReconstructionModule.o
> ../..//Modules/InputOutput/InputOutputModuleHDF.F90:1577:78
>
> 1577 | CALL H5DREAD_F( DATASET_ID, H5T_NATIVE_DOUBLE, Dataset,
> DATASIZE, HDFERR )
> |
> 1
> Error: There is no specific subroutine for the generic ‘h5dread_f’ at (1)
> ../..//Modules/InputOutput/InputOutputModuleHDF.F90:1526:78
>
> 1526 | CALL H5DREAD_F( DATASET_ID, H5T_NATIVE_DOUBLE, Dataset,
> DATASIZE, HDFERR )
> |
> 1
> Error: There is no specific subroutine for the generic ‘h5dread_f’ at (1)
> ../..//Modules/InputOutput/InputOutputModuleHDF.F90:1444:78
>
> 1444 | CALL H5DREAD_F( DATASET_ID, H5T_NATIVE_DOUBLE, Dataset,
> DATASIZE, HDFERR )
> |
> 1
> Error: There is no specific subroutine for the generic ‘h5dread_f’ at (1)
> make: *** [Makefile.Flash:171: InputOutputModuleHDF.o] Error 1
> make: *** Waiting for unfinished jobs....
>
> A setup internal error has occured, if possible please email the following
> debugging info to flash-x-users at lists.cels.anl.gov
> Arguments: ['/home/betelgeuse/FlashX/Flash-X/bin/setup.py', 'Relaxation',
> '-auto', '-3d', '+cartesian', '+cube16', '+thornado', 'nE=16', 'swE=1',
> 'nSpecies=6', 'nNodes=2', 'nMoments=4', 'momentClosure=MINERBO',
> 'thornadoOrder=ORDER_V', '+weaklib', '-parfile=flash.par']
> Python Version: 3.8.10
> Platform Details: linux
>
> I tried re-building HDF5 with 2003 features of Fortran enabled, but still
> no dice.
> Kiya, I noticed the following in the Miakefile.h you shared
> earlier: -DH5_USE_16_API
> Which version of HDF5 do you have installed (I was trying 1.8.22 with
> openmpi using gcc 9ish)?
>
> Best wishes,
> --------
> Ryan
>
>
> On Thu, Aug 29, 2024 at 5:53 AM Peter Manzella <peter.manzella at maine.edu>
> wrote:
>
>> Ryan,
>>
>> Depending on how this troubleshooting goes, will decide whether I decide
>> to do a fresh (re)start, I want to give it a chance before I go that route.
>> As for Kiya's suggestions, I have been working on them, I tried changing
>> "thornadoOrder=ORDER_1" to "thornadoOrder=ORDER_V" and along with that I
>> have looked in the object directory, and grabbed that output and placed it
>> in the file as Kiya, and you have suggested, see attached.
>>
>> On Thu, Aug 29, 2024 at 12:08 AM Ryan Farber <rjfarber at umich.edu> wrote:
>>
>>> Hi Peter,
>>>
>>> 1. Less of a Flash-X suggestion as much as personal life philosophy: yes
>>> sometimes the best path forward is a fresh (re)start. Along that vein, I've
>>> started the process of typing up a list of steps I need(ed) to take to "Get
>>> Flash-X to work" on my ubuntu virtual private server (which is definitely
>>> more of a pain since no packages are provided for me, but on the plus side
>>> I have full control over everything). I'm currently building lapack. (Will
>>> finish after I go to sleep likely.)
>>>
>>> 2. I don't know that you have to start over. Kiya mentioned two
>>> potentially helpful suggestions
>>>
>>> i. Try changing " thornadoOrder=ORDER_1" in your setup line to a
>>> different value
>>> ii. In your object directory, type "ls -l *.F90 > Flash-X-files.txt" and
>>> share that file with us. Then we can see if you the setup line correctly
>>> placed the files you need in the object directory, or if some are missing.
>>>
>>> Best wishes,
>>> --------
>>> Ryan
>>>
>>>
>>> On Wed, Aug 28, 2024 at 8:28 AM Peter Manzella <peter.manzella at maine.edu>
>>> wrote:
>>>
>>>> Kiya & Ryan,
>>>>
>>>> I finally got the chance to take a look at this, and what I'm gathering
>>>> is that my installation of thornado is not correct. I am not sure how to
>>>> troubleshoot this beyond "uninstall and reinstall" which I can assume is
>>>> not the way to go about this. Ryan mentioned that it may not be in the
>>>> proper system PATH, I'm assuming this could be corrected in the makefile
>>>> that is in the "sites" directory?
>>>>
>>>> I do hope that my struggles prove to be useful and helpful for those in
>>>> the future, so I very much thank you all for your help.
>>>>
>>>> On Tue, Aug 27, 2024 at 12:42 AM kiyarash Taghiniyarami <
>>>> kiyarash.niyarami at gmail.com> wrote:
>>>>
>>>>> Dear Peter & Ryan,
>>>>> No problem. I am just trying to help and hope it will be useful.
>>>>>
>>>>> I see in your setup syntax Thornado order is set to 1. Order one is
>>>>> not working properly (some files are missing in thornado order1 directory)
>>>>> since I asked Austin so far, he mentioned they tried to use orderV and then
>>>>> in flash.par setting v = 0.0 gives the same result as order1. So I am
>>>>> afraid Peter your setup is not complete yet and because of that
>>>>> wlEOSInversionModule.F90 is missing in the directory created by setup,
>>>>> check that out again.
>>>>>
>>>>> If you get ls of the obj directory (or whatever created by setup) you
>>>>> could see list of codes linked there and check if wlEOSInversion in present
>>>>> there or not.
>>>>>
>>>>> Best,
>>>>> Kiya
>>>>>
>>>>> On Tue, Aug 27, 2024 at 6:31 AM Peter Manzella <
>>>>> peter.manzella at maine.edu> wrote:
>>>>>
>>>>>> Ryan, Of course, many many thanks to Kiya, been extremely helpful.
>>>>>> And many thanks to you for lending a helping hand too! I didn't see your
>>>>>> email till very much after I had left my office, but noticed it and had to
>>>>>> come in to take care of
>>>>>> ZjQcmQRYFpfptBannerStart
>>>>>> This Message Is From an External Sender
>>>>>> This message came from outside your organization.
>>>>>>
>>>>>> ZjQcmQRYFpfptBannerEnd
>>>>>> Ryan,
>>>>>> Of course, many many thanks to Kiya, been extremely helpful. And many
>>>>>> thanks to you for lending a helping hand too! I didn't see your email till
>>>>>> very much after I had left my office, but noticed it and had to come in to
>>>>>> take care of some other things, so it is a bit late, sorry.
>>>>>> As asked (let me know if I didn't grab the right thing)
>>>>>> 1) screenshot of 'ls' in the problem directory:
>>>>>> [image: image.png]
>>>>>> 2) my setup command:
>>>>>>
>>>>>> ./setup Relaxation -auto -3d +cartesian +cube16 +thornado nE=16 swE=0
>>>>>> nSpecies=6 nNodes=2 nMoments=4 momentClosure=MINERBO thornadoOrder=ORDER_1
>>>>>> +weaklib -parfile=flash.par
>>>>>>
>>>>>> 3)full output in a compile.txt
>>>>>>
>>>>>> I really appreciate any and all help I can get, I've spent a bit on
>>>>>> trying to get through it, but quite often it felt like I was going in
>>>>>> circles.
>>>>>>
>>>>>> On Mon, Aug 26, 2024 at 4:42 PM Ryan Farber <rjfarber at umich.edu>
>>>>>> wrote:
>>>>>>
>>>>>>> Hi Peter,
>>>>>>>
>>>>>>> If you share the following I can take a look tonight:
>>>>>>> 1) screenshot of “ls” in your problem directory
>>>>>>> 2) your setup command
>>>>>>> 3) the full output and error streams of your compilation command
>>>>>>> (e.g., make 2>&1 compile.txt
>>>>>>>
>>>>>>> As an aside, thanks to Kiya for your kind contributions to this
>>>>>>> thread! I’m sure what you've provided will be useful in the future too!
>>>>>>>
>>>>>>> Best wishes,
>>>>>>> Ryan
>>>>>>>
>>>>>>> Sent from my iPhone
>>>>>>>
>>>>>>> On Aug 26, 2024, at 1:53 PM, Peter Manzella <
>>>>>>> peter.manzella at maine.edu> wrote:
>>>>>>>
>>>>>>>
>>>>>>> OK, that makes more sense, I'll need to make sure those are in the
>>>>>>> file, not command line. I went to setup after adding those, and have this
>>>>>>> error, its related to equation of state, and I haven't been able to find
>>>>>>> anything in documentation
>>>>>>> ZjQcmQRYFpfptBannerStart
>>>>>>> This Message Is From an External Sender
>>>>>>> This message came from outside your organization.
>>>>>>>
>>>>>>> ZjQcmQRYFpfptBannerEnd
>>>>>>> OK, that makes more sense, I'll need to make sure those are in the
>>>>>>> file, not command line. I went to setup after adding those, and have this
>>>>>>> error, its related to equation of state, and I haven't been able to find
>>>>>>> anything in documentation about it.
>>>>>>> <image.png>
>>>>>>>
>>>>>>> This is the sort of thing that is frustrating, not being able to
>>>>>>> find where I need to look to troubleshoot. I tried using grep to find it,
>>>>>>> I've looked in the documentation link you sent me (I already knew about
>>>>>>> that, but it wasn't helpful beyond the quick start), but couldn't find it.
>>>>>>> Is this more of a thornado issue? Cause like I said I'm not super
>>>>>>> acquainted with large codes that require so many moving pieces.
>>>>>>>
>>>>>>> On Mon, Aug 26, 2024 at 2:28 PM kiyarash Taghiniyarami <
>>>>>>> kiyarash.niyarami at gmail.com> wrote:
>>>>>>>
>>>>>>>> Dear Peter,
>>>>>>>> These are not for command line (If you mean "command line" as setup
>>>>>>>> for configuring a new run).
>>>>>>>> Before setup you need to make a directory in the Simulation unit
>>>>>>>> (/source/Simulation/SimulationMain). In that directory you need some codes
>>>>>>>> such as Simulation_data.F90, Simulation_init.F90, Simulation_initBlock.F90,
>>>>>>>> and etc.
>>>>>>>> Say you need the "Half" variable in the Simulation_initBlock.F90.
>>>>>>>> you can call it by KindModule from Thornado if you write the following in
>>>>>>>> that fortran code:
>>>>>>>> Use KindModule, only: Half
>>>>>>>> so you can use the "Half" anywhere in that
>>>>>>>> Simulation_initBlock.F90. It has nothing to do with typing in the command
>>>>>>>> line and hitting enter.
>>>>>>>> If I understand correctly what you mean, there are some setup
>>>>>>>> variables you can type in the command line (such as nxb,nyb, swE,nE and
>>>>>>>> etc.) which are different from modules. setup variables can be set up in
>>>>>>>> Config files in any physics subdirectories.
>>>>>>>>
>>>>>>>> There is documentation for Flashx as well:
>>>>>>>> https://urldefense.us/v3/__https://flash-x.github.io/Flash-X-docs/*__;Iw!!G_uCfscf7eWS!awZ6DTm9TMIMEGrykhFUnRiUVixmo9xV3cta33NmKainvaNUr4rbTQevuVFkh5eMV1N30xcsjk-nZKfWhbPn_Jf5zplyzBm_TH8nunBL$
>>>>>>>> <https://urldefense.us/v3/__https://flash-x.github.io/Flash-X-docs/*__;Iw!!G_uCfscf7eWS!cy5tKVb9Qwu2rLLCi1LNfkq2D5uVYlmB4FWF6x2Pvqvq1OrrRPvzAwx-yFHLivQcBbWQTRySdjTQzVXdJjzC_Qh1vl2zpGdoLrGAwyOT$>
>>>>>>>>
>>>>>>>> Kind regards,
>>>>>>>> Kiya
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> Peter Manzella
>>>>>>> PhD Candidate, Department of Physics and Astronomy
>>>>>>> 309 Bennett Hall
>>>>>>> University of Maine
>>>>>>> peter.manzella at maine.edu
>>>>>>>
>>>>>>> “If you run out of ideas follow the road; you'll get there.” – Edgar
>>>>>>> Allan Poe
>>>>>>> --
>>>>>>> Flash-X-users mailing list
>>>>>>> Flash-X-users at lists.cels.anl.gov
>>>>>>> https://urldefense.us/v3/__https://lists.cels.anl.gov/mailman/listinfo/flash-x-users__;!!G_uCfscf7eWS!awZ6DTm9TMIMEGrykhFUnRiUVixmo9xV3cta33NmKainvaNUr4rbTQevuVFkh5eMV1N30xcsjk-nZKfWhbPn_Jf5zplyzBm_TGABEu9d$
>>>>>>> <https://urldefense.us/v3/__https://lists.cels.anl.gov/mailman/listinfo/flash-x-users__;!!G_uCfscf7eWS!Z1_GXydE2pV62oyGpM2ZteP_zTQdp-c9MRnUEZgvDy2eM0cBnqD656HBLPAkAMqZu7096jmjWOZzHL2ARHhx_LB-ZMcFtJGRTFtRFBtj$>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>> --
>>>>>> Peter Manzella
>>>>>> PhD Candidate, Department of Physics and Astronomy
>>>>>> 309 Bennett Hall
>>>>>> University of Maine
>>>>>> peter.manzella at maine.edu
>>>>>>
>>>>>> “If you run out of ideas follow the road; you'll get there.” – Edgar
>>>>>> Allan Poe
>>>>>> --
>>>>>> Flash-X-users mailing list
>>>>>> Flash-X-users at lists.cels.anl.gov
>>>>>> https://urldefense.us/v3/__https://lists.cels.anl.gov/mailman/listinfo/flash-x-users__;!!G_uCfscf7eWS!awZ6DTm9TMIMEGrykhFUnRiUVixmo9xV3cta33NmKainvaNUr4rbTQevuVFkh5eMV1N30xcsjk-nZKfWhbPn_Jf5zplyzBm_TGABEu9d$
>>>>>>
>>>>>
>>>>
>>>> --
>>>> Peter Manzella
>>>> PhD Candidate, Department of Physics and Astronomy
>>>> 309 Bennett Hall
>>>> University of Maine
>>>> peter.manzella at maine.edu
>>>>
>>>> “If you run out of ideas follow the road; you'll get there.” – Edgar
>>>> Allan Poe
>>>>
>>>
>>
>> --
>> Peter Manzella
>> PhD Candidate, Department of Physics and Astronomy
>> 309 Bennett Hall
>> University of Maine
>> peter.manzella at maine.edu
>>
>> “If you run out of ideas follow the road; you'll get there.” – Edgar
>> Allan Poe
>>
>
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SUMMARY OF THE HDF5 CONFIGURATION
=================================
General Information:
-------------------
HDF5 Version: 1.14.3
Configured on: Wed Nov 22 23:30:45 +0330 2023
Configured by: taghinia at taghinia-virtual-machine
Host system: x86_64-pc-linux-gnu
Uname information: Linux taghinia-virtual-machine 5.15.0-76-generic #83~20.04.1-Ubuntu SMP Wed Jun 21 20:23:31 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
Byte sex: little-endian
Installation point: /home/taghinia/FLASH/HDF5/HDF5-install
Compiling Options:
------------------
Build Mode: production
Debugging Symbols: no
Asserts: no
Profiling: no
Optimization Level: high
Linking Options:
----------------
Libraries: static, shared
Statically Linked Executables:
LDFLAGS:
H5_LDFLAGS:
AM_LDFLAGS: -L/home/taghinia/FLASH/zlib/zlib-install/lib
Extra libraries: -lsz -lz -ldl -lm
Archiver: ar
AR_FLAGS: cr
Ranlib: ranlib
Languages:
----------
C: yes
C Compiler: /home/taghinia/FLASH/MPICH/mpich-install/bin/mpicc ( MPICH version 3.4.2 Configured with: ../src/configure -v --with-pkgversion='Ubuntu 9.4.0-1ubuntu1~20.04.2' --with-bugurl=file:///usr/share/doc/gcc-9/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,gm2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-9 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-9-9QDOt0/gcc-9-9.4.0/debian/tmp-nvptx/usr,hsa --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu built with gcc version 9.4.0 (Ubuntu 9.4.0-1ubuntu1~20.04.2))
CPPFLAGS:
H5_CPPFLAGS: -D_GNU_SOURCE -D_POSIX_C_SOURCE=200809L -DNDEBUG -UH5_DEBUG_API -I/home/taghinia/FLASH/HDF5/hdf5-1.14.3/src/H5FDsubfiling
AM_CPPFLAGS: -I/home/taghinia/FLASH/zlib/zlib-install/include
C Flags:
H5 C Flags: -std=c99 -Wall -Wcast-qual -Wconversion -Wextra -Wfloat-equal -Wformat=2 -Winit-self -Winvalid-pch -Wmissing-include-dirs -Wshadow -Wundef -Wwrite-strings -pedantic -Wno-c++-compat -Wlarger-than=2560 -Wlogical-op -Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wsync-nand -Wno-unsuffixed-float-constants -Wdouble-promotion -Wtrampolines -Wstack-usage=8192 -Wmaybe-uninitialized -Wdate-time -Warray-bounds=2 -Wc99-c11-compat -Wduplicated-cond -Whsa -Wnormalized -Wnull-dereference -Wunused-const-variable -Walloca -Walloc-zero -Wduplicated-branches -Wformat-overflow=2 -Wformat-truncation=1 -Wattribute-alias -Wcast-align=strict -Wshift-overflow=2 -Wattribute-alias=2 -Wmissing-profile -Wc11-c2x-compat -fstdarg-opt -s -Wbad-function-cast -Wcast-align -Wformat -Wimplicit-function-declaration -Wint-to-pointer-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wpacked -Wpointer-sign -Wpointer-to-int-cast -Wredundant-decls -Wstrict-prototypes -Wswitch -Wunused-but-set-variable -Wunused-variable -Wunused-function -Wunused-parameter -Wincompatible-pointer-types -Wint-conversion -Wshadow -Wrestrict -Wcast-function-type -Wmaybe-uninitialized -Wno-aggregate-return -Wno-inline -Wno-missing-format-attribute -Wno-missing-noreturn -Wno-overlength-strings -Wno-jump-misses-init -Wstrict-overflow=2 -Wno-suggest-attribute=const -Wno-suggest-attribute=noreturn -Wno-suggest-attribute=pure -Wno-suggest-attribute=format -Wno-suggest-attribute=cold -Wno-suggest-attribute=malloc -O3
AM C Flags:
Shared C Library: yes
Static C Library: yes
Fortran: yes
Fortran Compiler: /home/taghinia/FLASH/MPICH/mpich-install/bin/mpif90 ( MPICH version 3.4.2 Configured with: ../src/configure -v --with-pkgversion='Ubuntu 9.4.0-1ubuntu1~20.04.2' --with-bugurl=file:///usr/share/doc/gcc-9/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,gm2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-9 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-9-9QDOt0/gcc-9-9.4.0/debian/tmp-nvptx/usr,hsa --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu built with gcc version 9.4.0 (Ubuntu 9.4.0-1ubuntu1~20.04.2))
Fortran Flags:
H5 Fortran Flags: -std=f2008 -Waliasing -Wall -Wcharacter-truncation -Wextra -Wimplicit-interface -Wsurprising -Wunderflow -pedantic -Wintrinsics-std -Wimplicit-procedure -Wreal-q-constant -Wfunction-elimination -Wrealloc-lhs -Wrealloc-lhs-all -Wno-c-binding-type -Winteger-division -Wfrontend-loop-interchange -s -Wno-unused-dummy-argument -Wno-array-temporaries -O3
AM Fortran Flags:
Shared Fortran Library: yes
Static Fortran Library: yes
Module Directory: ${includedir}
C++: no
Java: no
Features:
---------
Parallel HDF5: yes
Parallel Filtered Dataset Writes: yes
Large Parallel I/O: yes
High-level library: yes
Dimension scales w/ new references: no
Build HDF5 Tests: yes
Build HDF5 Tools: yes
Build GIF Tools: no
Threadsafety: no
Default API mapping: v114
With deprecated public symbols: yes
I/O filters (external): deflate(zlib),szip(encoder)
Map (H5M) API: no
Direct VFD: no
Mirror VFD: no
Subfiling VFD: no
(Read-Only) S3 VFD: no
(Read-Only) HDFS VFD: no
Packages w/ extra debug output: none
API tracing: no
Using memory checker: no
Function stack tracing: no
Use file locking: best-effort
Strict file format checks: no
Optimization instrumentation: no
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