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#37626 - 08/22/19 04:47 AM Fortran runtime error: Bad value during integer read
sohyeon Offline
Forum Member

Registered: 08/21/19
Posts: 14
I made POPC input file through charmm-gui membrane builder , and I tried to running charmm " charmm -i step6.1_equilibration.inp" but it happen error.
As far as I know, the portran error is known by the unit setting, so in the step6.1_eqilibration.inp file

! Read PSF
open read unit 10 card name step5_assembly.psf
read psf unit 10 card

The unit has been adjusted(from 10 to 20). However, the same error still occurred.

How can I solve this situation?
please, Help me.

[sohyeon@theochem12 40popc]$ charmm -i step6.1_equilibration.inp
1
Chemistry at HARvard Macromolecular Mechanics
(CHARMM) - Developmental Version 38a1 September 30, 2012
SVN revision
Copyright(c) 1984-2001 President and Fellows of Harvard College
All Rights Reserved
Current operating system: Linux-2.6.32-279.14.1.el6.x86_64(x86_64)@the
Created on 8/22/19 at 17:30:44 by user: sohyeon

Maximum number of ATOMS: 1000000, and RESidues: 333333
RDTITL> * GENERATED BY CHARMM-GUI ([url=HTTP://WWW.CHARMM-GUI.ORG][url=HTTP://WWW.CHARMM-GUI.ORG][url=HTTP://WWW.CHARMM-GUI.ORG]HTTP://WWW.CHARMM-GUI.ORG[/url][/url][/url]) V2.0 ON AUG, 21. 2019. JOBID=156637331432
RDTITL> * INPUT FILES FOR EQUILIBRATION
RDTITL> *

CHARMM>

CHARMM> DIMENS CHSIZE 3000000 MAXRES 3000000
Size Original New
MAXA 1000000 3000000
MAXB 1000000 3000000
MAXT 2000000 6000000
MAXP 3000000 9000000
MAXIMP 500000 1500000
MAXNB 250000 750000
MAXPAD 1000000 3000000
MAXRES 333333 3000000
MAXSEG 125000 375000
MAXATC 500
MAXCB 1500
MAXCT 5500
MAXCP 10000
MAXCI 600
MAXCH 3200
MAXCN 125250
MAXCRT 333333 1000000

CHARMM>

CHARMM> ! Read topology and parameter files
CHARMM> stream toppar.str
VOPEN> Attempting to open::toppar.str::
OPNLGU> Unit 99 opened for READONLY access to toppar.str

INPUT STREAM SWITCHING TO UNIT 99
RDTITL> * GENERATED BY CHARMM-GUI ([url=HTTP://WWW.CHARMM-GUI.ORG][url=HTTP://WWW.CHARMM-GUI.ORG][url=HTTP://WWW.CHARMM-GUI.ORG]HTTP://WWW.CHARMM-GUI.ORG[/url][/url][/url]) V2.0 ON AUG, 21. 2019. JOBID=156637331432
RDTITL> * STREAM FILE FOR TOPOLOGY AND PARAMETER READING
RDTITL> *
Parameter: IN1 <- ""

CHARMM>

CHARMM> ! protein topology and parameter
CHARMM> !open read card unit 10 name toppar/top_all36_prot.rtf
CHARMM> !read rtf card unit 10
CHARMM>

CHARMM> !open read card unit 20 name toppar/par_all36m_prot.prm
CHARMM> !read para card unit 20 flex
CHARMM>

CHARMM> ! nucleic acids
CHARMM> !open read card unit 10 name toppar/top_all36_na.rtf
CHARMM> !read rtf card unit 10 append
CHARMM>

CHARMM> !open read card unit 20 name toppar/par_all36_na.prm
CHARMM> !read para card unit 20 append flex
CHARMM>

CHARMM> ! carbohydrates
CHARMM> !open read card unit 10 name toppar/top_all36_carb.rtf
CHARMM> !read rtf card unit 10 append
CHARMM>

CHARMM> !open read card unit 20 name toppar/par_all36_carb.prm
CHARMM> !read para card unit 20 append flex
CHARMM>

CHARMM> ! lipids
CHARMM> open read card unit 10 name toppar/top_all36_lipid.rtf
VOPEN> Attempting to open::toppar/top_all36_lipid.rtf::
OPNLGU> Unit 10 opened for READONLY access to toppar/top_all36_lipid.rtf

CHARMM> read rtf card unit 10
MAINIO> Residue topology file being read from unit 10.
TITLE> * \\\\\\\ CHARMM36 ALL-HYDROGEN LIPID TOPOLOGY FILE ///////
TITLE> * ALL COMMENTS AND QUESTIONS SHOULD BE SUBMITTED TO THE
TITLE> * PARAMETER FORUM AT THE CHARMM WEBSITE: www.CHARMM.ORG
TITLE> *

CHARMM>

CHARMM> open read card unit 20 name toppar/par_all36_lipid.prm
VOPEN> Attempting to open::toppar/par_all36_lipid.prm::
OPNLGU> Unit 20 opened for READONLY access to toppar/par_all36_lipid.prm

CHARMM> read para card unit 20

PARAMETER FILE BEING READ FROM UNIT 20
TITLE> * \\\\\\\ CHARMM36 ALL-HYDROGEN LIPID PARAMETER FILE ///////
TITLE> * ALL COMMENTS AND QUESTIONS SHOULD BE SUBMITTED TO THE
TITLE> * PARAMETER FORUM AT THE CHARMM WEBSITE: www.CHARMM.ORG
TITLE> *
PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared.

CHARMM>

CHARMM> ! CGENFF
CHARMM> !open read card unit 10 name toppar/top_all36_cgenff.rtf
CHARMM> !read rtf card unit 10 append
CHARMM>

CHARMM> !open read card unit 20 name toppar/par_all36_cgenff.prm
CHARMM> !read para card unit 20 append flex
CHARMM>

CHARMM> ! Interface FF
CHARMM> !open read card unit 10 name toppar/top_interface.rtf
CHARMM> !read rtf card unit 10 append
CHARMM>

CHARMM> !open read card unit 10 name toppar/par_interface.prm
CHARMM> !read para card unit 10 append flex
CHARMM>

CHARMM> ! Additional topologies and parameters for water and ions
CHARMM> !stream toppar/toppar_water_ions.str
CHARMM> !stream toppar/toppar_dum_noble_gases.str
CHARMM>

CHARMM> ! Additional topologies and parameters for protein
CHARMM> !stream toppar/toppar_all36_prot_d_aminoacids.str
CHARMM> !stream toppar/toppar_all36_prot_fluoro_alkanes.str
CHARMM> !stream toppar/toppar_all36_prot_heme.str
CHARMM> !stream toppar/toppar_all36_prot_na_combined.str
CHARMM> !stream toppar/toppar_all36_prot_retinol.str
CHARMM> !stream toppar/toppar_all36_prot_stapling.str
CHARMM> !stream toppar/toppar_all36_prot_modify_res.str
CHARMM>

CHARMM> ! Additional topologies and parameters for nucleic acids
CHARMM> !stream toppar/toppar_all36_na_nad_ppi.str
CHARMM> !stream toppar/toppar_all36_na_rna_modified.str
CHARMM>

CHARMM> ! Additional topologies and parameters for lipids
CHARMM> !stream toppar/toppar_all36_lipid_bacterial.str
CHARMM> !stream toppar/toppar_all36_lipid_cardiolipin.str
CHARMM> !stream toppar/toppar_all36_lipid_cholesterol.str
CHARMM> !stream toppar/toppar_all36_lipid_inositol.str
CHARMM> !stream toppar/toppar_all36_lipid_lps.str
CHARMM> !stream toppar/toppar_all36_lipid_miscellaneous.str
CHARMM> !stream toppar/toppar_all36_lipid_model.str
CHARMM> !stream toppar/toppar_all36_lipid_prot.str
CHARMM> !stream toppar/toppar_all36_lipid_pyrophosphate.str
CHARMM> !stream toppar/toppar_all36_lipid_sphingo.str
CHARMM> !stream toppar/toppar_all36_lipid_yeast.str
CHARMM> !stream toppar/toppar_all36_lipid_hmmm.str
CHARMM> !stream toppar/toppar_all36_lipid_detergent.str
CHARMM> !stream toppar/toppar_all36_lipid_ether.str
CHARMM>

CHARMM> ! Additional topologies and parameters for carbohydrates
CHARMM> !stream toppar/toppar_all36_carb_glycolipid.str
CHARMM> !stream toppar/toppar_all36_carb_glycopeptide.str
CHARMM> !stream toppar/toppar_all36_carb_imlab.str
CHARMM>

CHARMM> ! Additional topologies and parameters for spin/fluorophore labels
CHARMM> !stream toppar/toppar_all36_label_spin.str
CHARMM> !stream toppar/toppar_all36_label_fluorophore.str
CHARMM>

CHARMM>

VCLOSE: Closing unit 99 with status "KEEP"

RETURNING TO INPUT STREAM 5

CHARMM>

CHARMM> ! Read the system information
CHARMM> stream step3_size.str
VOPEN> Attempting to open::step3_size.str::
OPNLGU> Unit 99 opened for READONLY access to step3_size.str

INPUT STREAM SWITCHING TO UNIT 99
RDTITL> SET BOXTYPE = RECT
RDTITL> No title read.
Parameter: IN1 <- ""

CHARMM> SET BOXTYPE = RECT
Parameter: BOXTYPE <- "RECT"

CHARMM> SET XTLTYPE = TETRAGONAL
Parameter: XTLTYPE <- "TETRAGONAL"

CHARMM> SET A = 52.2685374
Parameter: A <- "52.2685374"

CHARMM> SET B = 52.2685374
Parameter: B <- "52.2685374"

CHARMM> SET C = 85
Parameter: C <- "85"

CHARMM> SET ALPHA = 90.0
Parameter: ALPHA <- "90.0"

CHARMM> SET BETA = 90.0
Parameter: BETA <- "90.0"

CHARMM> SET GAMMA = 90.0
Parameter: GAMMA <- "90.0"

CHARMM> SET ZCEN = 0
Parameter: ZCEN <- "0"

CHARMM> SET NLIPTOP = 40
Parameter: NLIPTOP <- "40"

CHARMM> SET NLIPBOT = 40
Parameter: NLIPBOT <- "40"

CHARMM> SET WBOXZ = 22.5
Parameter: WBOXZ <- "22.5"

CHARMM> SET WATBOXZ = 22.5
Parameter: WATBOXZ <- "22.5"

CHARMM> SET NCHARGE = 0
Parameter: NCHARGE <- "0"

VCLOSE: Closing unit 99 with status "KEEP"

RETURNING TO INPUT STREAM 5

CHARMM> stream step5_assembly.str
VOPEN> Attempting to open::step5_assembly.str::
OPNLGU> Unit 99 opened for READONLY access to step5_assembly.str

INPUT STREAM SWITCHING TO UNIT 99
RDTITL> SET BOXTYPE = RECT
RDTITL> No title read.
Parameter: IN1 <- ""

CHARMM> SET BOXTYPE = RECT
Parameter: BOXTYPE <- "RECT"

CHARMM> SET XTLTYPE = TETRAGONAL
Parameter: XTLTYPE <- "TETRAGONAL"

CHARMM> SET A = 52.2685374
Parameter: A <- "52.2685374"

CHARMM> SET B = 52.2685374
Parameter: B <- "52.2685374"

CHARMM> SET C = 85
Parameter: C <- "85"

CHARMM> SET ALPHA = 90.0
Parameter: ALPHA <- "90.0"

CHARMM> SET BETA = 90.0
Parameter: BETA <- "90.0"

CHARMM> SET GAMMA = 90.0
Parameter: GAMMA <- "90.0"

CHARMM> SET ZCEN = 0.0
Parameter: ZCEN <- "0.0"

CHARMM> SET NLIPTOP = 40
Parameter: NLIPTOP <- "40"

CHARMM> SET NLIPBOT = 40
Parameter: NLIPBOT <- "40"

CHARMM> SET NWATER = 3596
Parameter: NWATER <- "3596"

CHARMM> SET POSID = POT
Parameter: POSID <- "POT"

CHARMM> SET NEGID = CLA
Parameter: NEGID <- "CLA"

CHARMM> SET NPOS = 0
Parameter: NPOS <- "0"

CHARMM> SET NNEG = 0
Parameter: NNEG <- "0"

VCLOSE: Closing unit 99 with status "KEEP"

RETURNING TO INPUT STREAM 5

CHARMM>

CHARMM> ! Read PSF
CHARMM> open read unit 20 card name step5_assembly.psf
OPNLGU> Unit already open. The old file will be closed first.
VCLOSE: Closing unit 20 with status "KEEP"
VOPEN> Attempting to open::step5_assembly.psf::
OPNLGU> Unit 20 opened for READONLY access to step5_assembly.psf

CHARMM> read psf unit 20 card
MAINIO> Protein structure file being read from unit 20.
PSFRD2> Reading PSF in the expanded format.
TITLE> * GENERATED BY CHARMM-GUI ([url=HTTP://WWW.CHARMM-GUI.ORG][url=HTTP://WWW.CHARMM-GUI.ORG][url=HTTP://WWW.CHARMM-GUI.ORG]HTTP://WWW.CHARMM-GUI.ORG[/url][/url][/url]) V2.0 ON AUG, 21. 2019. JOB
TITLE> * ASSEMBLE PREVIOUSLY GENERATED COMPONENTS (LIPID BILAYER, PROTEIN, PORE WATER,
TITLE> * DATE: 8/21/19 3:45:56 CREATED BY USER: apache
TITLE> *
At line 231 of file /home/yongbin/bin/c38a1_plumed/source/io/psfres.src (unit = 10, file = 'step5_assembly.psf')
Fortran runtime error: Bad value during integer read

Top
#37627 - 08/22/19 05:31 AM Re: Fortran runtime error: Bad value during integer read [Re: sohyeon]
lennart Offline

Forum Member

Registered: 09/25/03
Posts: 4756
Loc: ~ 59N, 15E
Update to most recent CHARMM version.
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

Top
#37647 - 09/05/19 01:23 AM Re: Fortran runtime error: Bad value during integer read [Re: sohyeon]
sohyeon Offline
Forum Member

Registered: 08/21/19
Posts: 14
Thank you for your reply.

I used 3.8version, your comment means that I will download(install) version 41??


Edited by sohyeon (09/05/19 01:24 AM)

Top
#37650 - 09/05/19 04:59 PM Re: Fortran runtime error: Bad value during integer read [Re: sohyeon]
lennart Offline

Forum Member

Registered: 09/25/03
Posts: 4756
Loc: ~ 59N, 15E
www.charmm.org has information about obtaining CHARMM.
See http://charmm.chemistry.harvard.edu/charmm_lite.php for instructions on how to download the most recent freely available version of CHARMM.

Version 44b1 was released a couple of weeks ago. Version 41 is already 4 years old.
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

Top
#37659 - 09/24/19 06:24 AM Re: Fortran runtime error: Bad value during integer read [Re: sohyeon]
sohyeon Offline
Forum Member

Registered: 08/21/19
Posts: 14
I download recent version. Thank you .
But I cannot install recent charmm version.

The error occurred.


sohyeon@theochem11 charmm]$ ./configure
=====
swapping directories temporarily
~/charmm/build/cmake ~/charmm
=====
WARNING build directory not empty
moving to /export/home/sohyeon/charmm/build/cmake
press ctrl+c to abort
=====
configuration using cmake continues using
env /usr/local/bin/cmake -DCMAKE_INSTALL_PREFIX=/export/home/sohyeon/charmm -Din_place_install=ON /export/home/sohyeon/charmm

after configuration run make in
/export/home/sohyeon/charmm/build/cmake
to compile and link the charmm executable
=====
-- Could NOT find MKL (missing: MKL_INCLUDE_DIR)
CMake Error at tool/cmake/FindOpenMP_Fortran.cmake:128 (try_compile):
COPY_FILE specified on a srcdir type TRY_COMPILE
Call Stack (most recent call first):
tool/cmake/FindOpenMP_Fortran.cmake:176 (_OPENMP_GET_SPEC_DATE)
CMakeLists.txt:268 (find_package)


-- Could NOT find OPENMM (missing: OPENMM_INCLUDE_DIRS OPENMM_LIBRARIES)
-- Could NOT find OPENMM_CPU (missing: OPENMM_CPU_PLUGIN)
-- Could NOT find OPENMM_CUDA (missing: OPENMM_CUDA_PLUGIN)
-- Could NOT find OPENMM_OPENCL (missing: OPENMM_OPENCL_PLUGIN)
-- Could NOT find ExaFMM (missing: ExaFMM_LIBRARY)
CUDA_TOOLKIT_ROOT_DIR not found or specified
-- Could NOT find CUDA (missing: CUDA_TOOLKIT_ROOT_DIR CUDA_NVCC_EXECUTABLE CUDA_INCLUDE_DIRS CUDA_CUDART_LIBRARY)
-- OpenCL not found
-- full build chosen
CMake Error at CMakeLists.txt:814 (target_compile_definitions):
Unknown CMake command "target_compile_definitions".


-- Configuring incomplete, errors occurred!
=====
ERROR cmake configure failed
check cmake log files and try again




Installed cmake version is 2.8.10.2.
Is there a charmm installation error because the cmake version is too low?


Edited by sohyeon (09/24/19 07:15 AM)

Top
#37660 - 09/24/19 01:19 PM Re: Fortran runtime error: Bad value during integer read [Re: sohyeon]
rmv Online   content

Forum Member

Registered: 09/17/03
Posts: 8407
Loc: 39 03 48 N, 77 06 54 W
You may wish to try again, using an empty directory for the build process.

There should additional information on the error in build/cmake/CMakeFiles especially in the CMakeError.log file.

What compiler and MPI library versions were used?
_________________________
Rick Venable
computational chemist


Top
#37671 - 09/30/19 11:00 PM Re: Fortran runtime error: Bad value during integer read [Re: sohyeon]
sohyeon Offline
Forum Member

Registered: 08/21/19
Posts: 14
compiler is gnu.

I erased all charmm folder using rm -r charmm, redownload charmm install file and moved my cluster.
I ran ./cofigure on the created charmm folder but still got a similar error.

[sohyeon@theochem11 charmm]$ ./configure
=====
swapping directories temporarily
~/charmm/build/cmake ~/charmm
=====
WARNING build directory not empty
moving to /export/home/sohyeon/charmm/build/cmake
press ctrl+c to abort
=====
configuration using cmake continues using
env /usr/local/bin/cmake -DCMAKE_INSTALL_PREFIX=/export/home/sohyeon/charmm -Din_place_install=ON /export/home/sohyeon/charmm

after configuration run make in
/export/home/sohyeon/charmm/build/cmake
to compile and link the charmm executable
=====
-- The C compiler identification is GNU 4.4.6
-- The CXX compiler identification is GNU 4.4.6
-- The Fortran compiler identification is GNU
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working Fortran compiler: /usr/bin/gfortran
-- Check for working Fortran compiler: /usr/bin/gfortran -- works
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Checking whether /usr/bin/gfortran supports Fortran 90
-- Checking whether /usr/bin/gfortran supports Fortran 90 -- yes
-- Could NOT find MKL (missing: MKL_INCLUDE_DIR)
-- Found FFTW: /usr/local/include
-- Found FFTWF: /usr/local/lib/libfftw3f.a
-- Found MPI_C: /opt/openmpi/lib/libmpi.so;/usr/lib64/libibverbs.so;/usr/lib64/libdat.so;/usr/lib64/librt.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.so;/usr/lib64/libm.so;/usr/lib64/libdl.so;/usr/lib64/libm.so;/usr/lib64/librt.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.so;/usr/lib64/libm.so;/usr/lib64/libdl.so
-- Found MPI_CXX: /opt/openmpi/lib/libmpi_cxx.so;/opt/openmpi/lib/libmpi.so;/usr/lib64/libibverbs.so;/usr/lib64/libdat.so;/usr/lib64/librt.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.so;/usr/lib64/libm.so;/usr/lib64/libdl.so;/usr/lib64/libm.so;/usr/lib64/librt.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.so;/usr/lib64/libm.so;/usr/lib64/libdl.so
-- Found MPI_Fortran: /opt/openmpi/lib/libmpi_f90.so;/opt/openmpi/lib/libmpi_f77.so;/opt/openmpi/lib/libmpi.so;/usr/lib64/libibverbs.so;/usr/lib64/libdat.so;/usr/lib64/librt.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.so;/usr/lib64/libm.so;/usr/lib64/libdl.so;/usr/lib64/libm.so;/usr/lib64/librt.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.so;/usr/lib64/libm.so;/usr/lib64/libdl.so
-- Try OpenMP C flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Found OpenMP: -fopenmp
-- Try OpenMP Fortran flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
CMake Error at tool/cmake/FindOpenMP_Fortran.cmake:128 (try_compile):
COPY_FILE specified on a srcdir type TRY_COMPILE
Call Stack (most recent call first):
tool/cmake/FindOpenMP_Fortran.cmake:176 (_OPENMP_GET_SPEC_DATE)
CMakeLists.txt:268 (find_package)


-- Found OpenMP_Fortran: -fopenmp
-- Could NOT find OPENMM (missing: OPENMM_INCLUDE_DIRS OPENMM_LIBRARIES)
-- Could NOT find OPENMM_CPU (missing: OPENMM_CPU_PLUGIN)
-- Could NOT find OPENMM_CUDA (missing: OPENMM_CUDA_PLUGIN)
-- Could NOT find OPENMM_OPENCL (missing: OPENMM_OPENCL_PLUGIN)
-- Could NOT find ExaFMM (missing: ExaFMM_LIBRARY)
CUDA_TOOLKIT_ROOT_DIR not found or specified
-- Could NOT find CUDA (missing: CUDA_TOOLKIT_ROOT_DIR CUDA_NVCC_EXECUTABLE CUDA_INCLUDE_DIRS CUDA_CUDART_LIBRARY)
-- Looking for CL_VERSION_2_2
-- Looking for CL_VERSION_2_2 - not found
-- Looking for CL_VERSION_2_1
-- Looking for CL_VERSION_2_1 - not found
-- Looking for CL_VERSION_2_0
-- Looking for CL_VERSION_2_0 - not found
-- Looking for CL_VERSION_1_2
-- Looking for CL_VERSION_1_2 - not found
-- Looking for CL_VERSION_1_1
-- Looking for CL_VERSION_1_1 - not found
-- Looking for CL_VERSION_1_0
-- Looking for CL_VERSION_1_0 - not found
-- OpenCL not found
-- full build chosen
CMake Error at CMakeLists.txt:814 (target_compile_definitions):
Unknown CMake command "target_compile_definitions".


-- Configuring incomplete, errors occurred!
=====
ERROR cmake configure failed
check cmake log files and try again.


I don't know exactly what it means to empty the directory to create a process.
(Is it right erase charmm/build? or Do I need to reset the build directory process?)


This is a list in the charmm folder in my cluster.
[sohyeon@theochem11 charmm]$ ls
CMakeLists.txt ChangeLogs build configure doc install.com source sphinxdoc support test tool toppar


Edited by sohyeon (09/30/19 11:01 PM)

Top
#37672 - 10/01/19 12:17 PM Re: Fortran runtime error: Bad value during integer read [Re: sohyeon]
rmv Online   content

Forum Member

Registered: 09/17/03
Posts: 8407
Loc: 39 03 48 N, 77 06 54 W
I suggest following the guidelines in the CHARMM documentation for the cmake build process; I use a similar process for my builds. A new directory is created, and the configure command is run in the new, empty directory.

Do not erase charmm/build, or all of the charmm tree, just the contents of e.g. charmm/build/cmake before attempting to build charmm again in that same directory.

First, however, check the contents of

charmm/build/cmake/CMakeFiles/CMakeError.log

for additional error messages about the problems encountered.
_________________________
Rick Venable
computational chemist


Top
#37673 - 10/02/19 04:23 AM Re: Fortran runtime error: Bad value during integer read [Re: sohyeon]
sohyeon Offline
Forum Member

Registered: 08/21/19
Posts: 14
This is charmm/build/cmake/CMakeFiles/CMakeError.log

Determining if the CL_VERSION_2_2 exist failed with the following output:
Change Dir: /export/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp

Run Build Command:/usr/bin/gmake "cmTryCompileExec1710634290/fast"
/usr/bin/gmake -f CMakeFiles/cmTryCompileExec1710634290.dir/build.make CMakeFiles/cmTryCompileExec1710634290.dir/build
gmake[1]: Entering directory `/state/partition1/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp'
/usr/local/bin/cmake -E cmake_progress_report /export/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp/CMakeFiles 1
Building C object CMakeFiles/cmTryCompileExec1710634290.dir/CheckSymbolExists.c.o
/usr/bin/cc -o CMakeFiles/cmTryCompileExec1710634290.dir/CheckSymbolExists.c.o -c /export/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp/CheckSymbolExists.c
/export/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp/CheckSymbolExists.c:2:47: error: OpenCL_INCLUDE_DIR-NOTFOUND/CL/cl.h: No such file or directory
/export/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp/CheckSymbolExists.c: In function ‘main’:
/export/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp/CheckSymbolExists.c:8: error: ‘CL_VERSION_2_2’ undeclared (first use in this function)
/export/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp/CheckSymbolExists.c:8: error: (Each undeclared identifier is reported only once
/export/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp/CheckSymbolExists.c:8: error: for each function it appears in.)
gmake[1]: *** [CMakeFiles/cmTryCompileExec1710634290.dir/CheckSymbolExists.c.o] error 1
gmake[1]: Leaving directory `/state/partition1/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp'
gmake: *** [cmTryCompileExec1710634290/fast] error 2

File /export/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp/CheckSymbolExists.c:
/* */
#include

int main(int argc, char** argv)
{
(void)argv;
#ifndef CL_VERSION_2_2
return ((int*)(&CL_VERSION_2_2))[argc];
#else
(void)argc;
return 0;
#endif
}

Determining if the CL_VERSION_2_1 exist failed with the following output:
Change Dir: /export/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp

Run Build Command:/usr/bin/gmake "cmTryCompileExec1468820692/fast"
/usr/bin/gmake -f CMakeFiles/cmTryCompileExec1468820692.dir/build.make CMakeFiles/cmTryCompileExec1468820692.dir/build
gmake[1]: Entering directory `/state/partition1/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp'
/usr/local/bin/cmake -E cmake_progress_report /export/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp/CMakeFiles 1
Building C object CMakeFiles/cmTryCompileExec1468820692.dir/CheckSymbolExists.c.o
/usr/bin/cc -o CMakeFiles/cmTryCompileExec1468820692.dir/CheckSymbolExists.c.o -c /export/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp/CheckSymbolExists.c
/export/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp/CheckSymbolExists.c:2:47: error: OpenCL_INCLUDE_DIR-NOTFOUND/CL/cl.h: No such file or directory
/export/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp/CheckSymbolExists.c: In function ‘main’:
/export/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp/CheckSymbolExists.c:8: error: ‘CL_VERSION_2_1’ undeclared (first use in this function)
/export/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp/CheckSymbolExists.c:8: error: (Each undeclared identifier is reported only once
/export/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp/CheckSymbolExists.c:8: error: for each function it appears in.)
gmake[1]: *** [CMakeFiles/cmTryCompileExec1468820692.dir/CheckSymbolExists.c.o] error 1
gmake[1]: Leaving directory `/state/partition1/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp'
gmake: *** [cmTryCompileExec1468820692/fast] error 2

File /export/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp/CheckSymbolExists.c:
/* */
#include

int main(int argc, char** argv)
{
(void)argv;
#ifndef CL_VERSION_2_1
return ((int*)(&CL_VERSION_2_1))[argc];
#else
(void)argc;
return 0;
#endif
}

Determining if the CL_VERSION_2_0 exist failed with the following output:
Change Dir: /export/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp

Run Build Command:/usr/bin/gmake "cmTryCompileExec2996316082/fast"
/usr/bin/gmake -f CMakeFiles/cmTryCompileExec2996316082.dir/build.make CMakeFiles/cmTryCompileExec2996316082.dir/build
gmake[1]: Entering directory `/state/partition1/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp'
/usr/local/bin/cmake -E cmake_progress_report /export/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp/CMakeFiles 1
Building C object CMakeFiles/cmTryCompileExec2996316082.dir/CheckSymbolExists.c.o
/usr/bin/cc -o CMakeFiles/cmTryCompileExec2996316082.dir/CheckSymbolExists.c.o -c /export/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp/CheckSymbolExists.c
/export/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp/CheckSymbolExists.c:2:47: error: OpenCL_INCLUDE_DIR-NOTFOUND/CL/cl.h: No such file or directory
/export/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp/CheckSymbolExists.c: In function ‘main’:
/export/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp/CheckSymbolExists.c:8: error: ‘CL_VERSION_2_0’ undeclared (first use in this function)
/export/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp/CheckSymbolExists.c:8: error: (Each undeclared identifier is reported only once
/export/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp/CheckSymbolExists.c:8: error: for each function it appears in.)
gmake[1]: *** [CMakeFiles/cmTryCompileExec2996316082.dir/CheckSymbolExists.c.o] error 1
gmake[1]: Leaving directory `/state/partition1/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp'
gmake: *** [cmTryCompileExec2996316082/fast] error 2

File /export/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp/CheckSymbolExists.c:
/* */
#include


#include

int main(int argc, char** argv)
{
(void)argv;
#ifndef CL_VERSION_2_0
return ((int*)(&CL_VERSION_2_0))[argc];
#else
(void)argc;
return 0;
#endif
}

Determining if the CL_VERSION_1_2 exist failed with the following output:
Change Dir: /export/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp

Run Build Command:/usr/bin/gmake "cmTryCompileExec1231046631/fast"
/usr/bin/gmake -f CMakeFiles/cmTryCompileExec1231046631.dir/build.make CMakeFiles/cmTryCompileExec1231046631.dir/build
gmake[1]: Entering directory `/state/partition1/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp'
/usr/local/bin/cmake -E cmake_progress_report /export/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp/CMakeFiles 1
Building C object CMakeFiles/cmTryCompileExec1231046631.dir/CheckSymbolExists.c.o
/usr/bin/cc -o CMakeFiles/cmTryCompileExec1231046631.dir/CheckSymbolExists.c.o -c /export/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp/CheckSymbolExists.c
/export/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp/CheckSymbolExists.c:2:47: error: OpenCL_INCLUDE_DIR-NOTFOUND/CL/cl.h: No such file or directory
/export/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp/CheckSymbolExists.c: In function ‘main’:
/export/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp/CheckSymbolExists.c:8: error: ‘CL_VERSION_1_2’ undeclared (first use in this function)
/export/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp/CheckSymbolExists.c:8: error: (Each undeclared identifier is reported only once
/export/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp/CheckSymbolExists.c:8: error: for each function it appears in.)
gmake[1]: *** [CMakeFiles/cmTryCompileExec1231046631.dir/CheckSymbolExists.c.o] 오류 1
gmake[1]: Leaving directory `/state/partition1/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp'
gmake: *** [cmTryCompileExec1231046631/fast] 오류 2

File /export/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp/CheckSymbolExists.c:
/* */
#include

int main(int argc, char** argv)
{
(void)argv;
#ifndef CL_VERSION_1_2
return ((int*)(&CL_VERSION_1_2))[argc];
#else
(void)argc;
return 0;
#endif
}

Determining if the CL_VERSION_1_1 exist failed with the following output:
Change Dir: /export/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp

Run Build Command:/usr/bin/gmake "cmTryCompileExec83846168/fast"
/usr/bin/gmake -f CMakeFiles/cmTryCompileExec83846168.dir/build.make CMakeFiles/cmTryCompileExec83846168.dir/build
gmake[1]: Entering directory `/state/partition1/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp'
/usr/local/bin/cmake -E cmake_progress_report /export/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp/CMakeFiles 1
Building C object CMakeFiles/cmTryCompileExec83846168.dir/CheckSymbolExists.c.o
/usr/bin/cc -o CMakeFiles/cmTryCompileExec83846168.dir/CheckSymbolExists.c.o -c /export/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp/CheckSymbolExists.c
/export/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp/CheckSymbolExists.c:2:47: error: OpenCL_INCLUDE_DIR-NOTFOUND/CL/cl.h: No such file or directory
/export/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp/CheckSymbolExists.c: In function ‘main’:
/export/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp/CheckSymbolExists.c:8: error: ‘CL_VERSION_1_1’ undeclared (first use in this function)
/export/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp/CheckSymbolExists.c:8: error: (Each undeclared identifier is reported only once
/export/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp/CheckSymbolExists.c:8: error: for each function it appears in.)
gmake[1]: *** [CMakeFiles/cmTryCompileExec83846168.dir/CheckSymbolExists.c.o] 오류 1
gmake[1]: Leaving directory `/state/partition1/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp'
gmake: *** [cmTryCompileExec83846168/fast] error 2

File /export/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp/CheckSymbolExists.c:
/* */
#include

int main(int argc, char** argv)
{
(void)argv;
#ifndef CL_VERSION_1_1
return ((int*)(&CL_VERSION_1_1))[argc];
#else
(void)argc;
return 0;
#endif
}

Determining if the CL_VERSION_1_0 exist failed with the following output:
Change Dir: /export/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp

Run Build Command:/usr/bin/gmake "cmTryCompileExec1353340653/fast"
/usr/bin/gmake -f CMakeFiles/cmTryCompileExec1353340653.dir/build.make CMakeFiles/cmTryCompileExec1353340653.dir/build
gmake[1]: Entering directory `/state/partition1/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp'
/usr/local/bin/cmake -E cmake_progress_report /export/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp/CMakeFiles 1
Building C object CMakeFiles/cmTryCompileExec1353340653.dir/CheckSymbolExists.c.o
/usr/bin/cc -o CMakeFiles/cmTryCompileExec1353340653.dir/CheckSymbolExists.c.o -c /export/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp/CheckSymbolExists.c
/export/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp/CheckSymbolExists.c:2:47: error: OpenCL_INCLUDE_DIR-NOTFOUND/CL/cl.h: No such file or directory
/export/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp/CheckSymbolExists.c: In function ‘main’:
/export/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp/CheckSymbolExists.c:8: error: ‘CL_VERSION_1_0’ undeclared (first use in this function)
/export/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp/CheckSymbolExists.c:8: error: (Each undeclared identifier is reported only once
/export/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp/CheckSymbolExists.c:8: error: for each function it appears in.)
gmake[1]: *** [CMakeFiles/cmTryCompileExec1353340653.dir/CheckSymbolExists.c.o] error 1
gmake[1]: Leaving directory `/state/partition1/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp'
gmake: *** [cmTryCompileExec1353340653/fast] error 2

File /export/home/sohyeon/charmm/build/cmake/CMakeFiles/CMakeTmp/CheckSymbolExists.c:
/* */
#include

int main(int argc, char** argv)
{
(void)argv;
#ifndef CL_VERSION_1_0
return ((int*)(&CL_VERSION_1_0))[argc];
#else
(void)argc;
return 0;
#endif
}

To solve error,
Should I make CheckSymbolExists ?; e.g. mkdir CheckSymbolExists





I followed the guidelines in the CHARMM documentaion for the cmake build process
;(http://bitly.kr/lYTtg2j)
But It still got the same error.

Top
#37674 - 10/02/19 09:43 AM Re: Fortran runtime error: Bad value during integer read [Re: sohyeon]
bucknerj Offline

Forum Member

Registered: 04/16/13
Posts: 20
Your cmake and gcc versions are too old.

Whatever the current versions for RedHat 7 are should work:
cmake 2.8.12.2 and above works
gcc 4.8.5 and above works

You can get the latest binaries for cmake from
https://cmake.org/download/

Be sure to put the path to the latest cmake in your PATH environment variable before the path to the old one.

Or, you can use the 'configure' argument
'--cmake <path to cmake>'

How to get up to date gcc binaries will depend on your system.
_________________________
Josh Buckner
Brooks Lab
University of Michigan

Top
#37675 - 10/02/19 11:32 AM Re: Fortran runtime error: Bad value during integer read [Re: sohyeon]
rmv Online   content

Forum Member

Registered: 09/17/03
Posts: 8407
Loc: 39 03 48 N, 77 06 54 W
First, a reminder; larger, text based listings should be attached as .txt files, rather than included directly in the post. Please review the READ BEFORE POSTING topic.

Note that once you upgrade your GCC compiler suite, to run CHARMM in parallel you will probably also need to build an MPI library with the same GCC suite being used to build CHARMM, and with Fortran90 support enabled.
_________________________
Rick Venable
computational chemist


Top
#37728 - 11/25/19 10:14 PM Re: Fortran runtime error: Bad value during integer read [Re: sohyeon]
sohyeon Offline
Forum Member

Registered: 08/21/19
Posts: 14
I am so sorry, I forgot using the .txt files.


I set Environment Variable of gcc and cmake

export PATH=./:~/GCC-7.3.0/bin/:$PATH
export PATH=./:~/cmake-3.13.4-Linux-x86_64/bin/:$PATH


so

gcc --version : 7.7.0
cmake --version : 3.13.4

I followed "charmm/doc/cmake.info"
Configuration:: The First Step

$ mkdir charmm-build
$ ls
charmm charmm-build

From the new build directory, invoke the configure script with the desired
options.

$ cd charmm-build
$ ../charmm/configure ...
-> no occurred error in this step.


Compilation:: The Second Step
$ make -j3
-> occurred error like this..
.
.
.
[ 83%] Building Fortran object CMakeFiles/charmm_fortran.dir/lambdadyn.F90.o
[ 83%] Building Fortran object CMakeFiles/charmm_fortran.dir/rmsdyn.F90.o
[ 83%] Building Fortran object CMakeFiles/charmm_fortran.dir/replica.F90.o
[ 83%] Building Fortran object CMakeFiles/charmm_fortran.dir/umb.F90.o
[ 83%] Building Fortran object CMakeFiles/charmm_fortran.dir/secstr.F90.o
[ 83%] Building Fortran object CMakeFiles/charmm_fortran.dir/images.F90.o
[ 84%] Building Fortran object CMakeFiles/charmm_fortran.dir/upimag.F90.o
[ 84%] Building Fortran object CMakeFiles/charmm_fortran.dir/corman2.F90.o
[ 84%] Building Fortran object CMakeFiles/charmm_fortran.dir/genpsf.F90.o
[ 84%] Building Fortran object CMakeFiles/charmm_fortran.dir/cmds.F90.o
[ 84%] Building Fortran object CMakeFiles/charmm_fortran.dir/eadumb.F90.o
[ 84%] Building Fortran object CMakeFiles/charmm_fortran.dir/eval.F90.o
[ 84%] Building Fortran object CMakeFiles/charmm_fortran.dir/nbndgcm.F90.o
[ 84%] Building Fortran object CMakeFiles/charmm_fortran.dir/nbndgc.F90.o
[ 84%] Building Fortran object CMakeFiles/charmm_fortran.dir/colfft_kernel.F90.o
[ 84%] Building Fortran object CMakeFiles/charmm_fortran.dir/ancsol.F90.o
[ 84%] Building Fortran object CMakeFiles/charmm_fortran.dir/rdfsol.F90.o
/export/home/sohyeon/charmm/source/nbonds/colfft_kernel_precision.inc:475.6:
Included at /export/home/sohyeon/charmm-build/colfft_kernel.F90:111:

!$omp end atomic
1
Error: Unclassifiable OpenMP directive at (1)
/export/home/sohyeon/charmm/source/nbonds/colfft_kernel_precision.inc:475.6:
Included at /export/home/sohyeon/charmm-build/colfft_kernel.F90:117:

!$omp end atomic
1
Error: Unclassifiable OpenMP directive at (1)
make[2]: *** [CMakeFiles/charmm_fortran.dir/colfft_kernel.F90.o] error 1
make[2]: *** 끝나지 않은 작업을 기다리고 있습니다....
make[1]: *** [CMakeFiles/charmm_fortran.dir/all] error 2
make: *** [all] error 2


So I tried to again
[sohyeon@theochem11 charmm-build]$ make -j3
[ 1%] Built target qchem
[ 1%] Built target charmm_c
[ 1%] Built target charmm_cxx
[ 1%] Building Fortran object CMakeFiles/charmm_fortran.dir/primsh.F90.o
[ 1%] Building Fortran object CMakeFiles/charmm_fortran.dir/colfft_kernel.F90.o
[ 1%] Building Fortran object CMakeFiles/charmm_fortran.dir/modpsf.F90.o
/export/home/sohyeon/charmm/source/nbonds/colfft_kernel_precision.inc:475.6:
Included at /export/home/sohyeon/charmm-build/colfft_kernel.F90:111:

!$omp end atomic
1
Error: Unclassifiable OpenMP directive at (1)
/export/home/sohyeon/charmm/source/nbonds/colfft_kernel_precision.inc:475.6:
Included at /export/home/sohyeon/charmm-build/colfft_kernel.F90:117:

!$omp end atomic
1
Error: Unclassifiable OpenMP directive at (1)
make[2]: *** [CMakeFiles/charmm_fortran.dir/colfft_kernel.F90.o] error 1
make[2]: *** 끝나지 않은 작업을 기다리고 있습니다....
make[1]: *** [CMakeFiles/charmm_fortran.dir/all] error 2
make: *** [all] error 2


How do I solve it?


Edited by sohyeon (11/26/19 06:14 AM)

Top
#37734 - 11/26/19 12:22 PM Re: Fortran runtime error: Bad value during integer read [Re: sohyeon]
rmv Online   content

Forum Member

Registered: 09/17/03
Posts: 8407
Loc: 39 03 48 N, 77 06 54 W
Not sure, but these version numbers in your post don't match--
Code:
export PATH=./:~/GCC-7.3.0/bin/:$PATH

gcc --version : 7.7.0

The error could be related to the compiler support for OpenMP threads, so I would probably try a different compiler. It is not an error I've seen before, but I tend to use the Intel suite more than GCC.
_________________________
Rick Venable
computational chemist


Top
#37737 - 11/26/19 08:17 PM Re: Fortran runtime error: Bad value during integer read [Re: sohyeon]
sohyeon Offline
Forum Member

Registered: 08/21/19
Posts: 14
I wrote it wrong.

Not gcc --version:7.7.0 but gcc--version : 7.3.0

($ gcc --version
gcc (GCC) 7.3.0
Copyright (C) 2017 Free Software Foundation, Inc.)

I will try a different complier.

Top
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