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We currently only support deleting an event if it is triggered and not
re-scheduled. This is fine for most native code. However, there are
cases where Python needs to count references to make sure that the
Python object stays live while the native object is live.
Generalise the mechanism used to implement by adding reference
counting hooks to the event base class:
* Event::acquire() / Event::acquireImpl()
* Event::release() / Event::releaseImpl()
These calls can be used to implement both reference counting and the
existing AutoDelete functionality. The default implementation in Event
maintains backwards compatibility with the existing AutoDelete feature
by ignoring acquireImpl() and deleting the event on releaseImpl() if
it isn't scheduled anymore.
Since AutoDelete functionality is no longer the only way events can be
managed, this change introduces the new Managed flag. This flag
activates automatic memory management. The acquireImpl()/releaseImpl()
methods are only called from acquire()/release() it is set. To
maintain backwards compatibility, AutoDelete is used as an alias for
Managed.
Change-Id: I5637984c906a9d44c22780712cf1c521b8297149
Signed-off-by: Andreas Sandberg <andreas.sandberg@arm.com>
Reviewed-by: Curtis Dunham <curtis.dunham@arm.com>
Reviewed-on: https://gem5-review.googlesource.com/3221
Reviewed-by: Jason Lowe-Power <jason@lowepower.com>
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Compiling gem5 with recent version of clang (4 and 5) triggers
warnings that are treated as errors:
* Global templatized static functions result in a warning if they
are not used. These should either be declared as static inline or
without the static identifier to avoid the warning.
* Some templatized classes contain static variables. The
instantiated versions of these variables / templates need to be
explicitly declared to avoid a compiler warning.
Change-Id: Ie8261144836e94ebab7ea04ccccb90927672c257
Signed-off-by: Andreas Sandberg <andreas.sandberg@arm.com>
Reviewed-by: Curtis Dunham <curtis.dunham@arm.com>
Reviewed-on: https://gem5-review.googlesource.com/3420
Reviewed-by: Jason Lowe-Power <jason@lowepower.com>
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Clang's UBSAN implementation complains about macros that expand to
expressions that contain 'defined'. Explicitly set the various feature
macros to 1 or 0 to avoid this issue.
Change-Id: Iba239dacfe526c43ab9c5da5183a350fc4fdc57d
Signed-off-by: Andreas Sandberg <andreas.sandberg@arm.com>
Reviewed-by: Andreas Hansson <andreas.hansson@arm.com>
Reviewed-by: Curtis Dunham <curtis.dunham@arm.com>
Reviewed-on: https://gem5-review.googlesource.com/3241
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This commit fixes a stack-buffer underflow
by fixing the way the array is indexed.
Change-Id: I44400e2b99a2f8e1f48f673cd110b9dcd6480a72
Reviewed-on: https://gem5-review.googlesource.com/3040
Reviewed-by: Jason Lowe-Power <jason@lowepower.com>
Reviewed-by: Andreas Sandberg <andreas.sandberg@arm.com>
Reviewed-by: Curtis Dunham <curtis.dunham@arm.com>
Maintainer: Brandon Potter <Brandon.Potter@amd.com>
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Remove SWIG guards and SWIG-specific C++ code.
Change-Id: Icaad6720513b6f48153727ef3f70e0dba0df4bee
Signed-off-by: Andreas Sandberg <andreas.sandberg@arm.com>
Reviewed-by: Andreas Hansson <andreas.hansson@arm.com>
Reviewed-by: Curtis Dunham <curtis.dunham@arm.com>
Reviewed-on: https://gem5-review.googlesource.com/2921
Reviewed-by: Jason Lowe-Power <jason@lowepower.com>
Reviewed-by: Tony Gutierrez <anthony.gutierrez@amd.com>
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Use the PyBind11 wrapping infrastructure instead of SWIG to generate
wrappers for functionality that needs to be exported to Python. This
has several benefits:
* PyBind11 can be redistributed with gem5, which means that we have
full control of the version used. This avoid a large number of
hard-to-debug SWIG issues we have seen in the past.
* PyBind11 doesn't rely on a custom C++ parser, instead it relies on
wrappers being explicitly declared in C++. The leads to slightly
more boiler-plate code in manually created wrappers, but doesn't
doesn't increase the overall code size. A big benefit is that this
avoids strange compilation errors when SWIG doesn't understand
modern language features.
* Unlike SWIG, there is no risk that the wrapper code incorporates
incorrect type casts (this has happened on numerous occasions in
the past) since these will result in compile-time errors.
As a part of this change, the mechanism to define exported methods has
been redesigned slightly. New methods can be exported either by
declaring them in the SimObject declaration and decorating them with
the cxxMethod decorator or by adding an instance of
PyBindMethod/PyBindProperty to the cxx_exports class variable. The
decorator has the added benefit of making it possible to add a
docstring and naming the method's parameters.
The new wrappers have the following known issues:
* Global events can't be memory managed correctly. This was the
case in SWIG as well.
Change-Id: I88c5a95b6cf6c32fa9e1ad31dfc08b2e8199a763
Signed-off-by: Andreas Sandberg <andreas.sandberg@arm.com>
Reviewed-by: Andreas Hansson <andreas.hansson@arm.com>
Reviewed-by: Andrew Bardsley <andrew.bardsley@arm.com>
Reviewed-on: https://gem5-review.googlesource.com/2231
Reviewed-by: Tony Gutierrez <anthony.gutierrez@amd.com>
Reviewed-by: Pierre-Yves Péneau <pierre-yves.peneau@lirmm.fr>
Reviewed-by: Jason Lowe-Power <jason@lowepower.com>
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Allow global stats such as sim_seconds in power equations to make it
possible to convert from event stats to rate stats.
Change-Id: I429abe0ffadc0dbd162eb39e0897143be472ef65
Signed-off-by: Andreas Sandberg <andreas.sandberg@arm.com>
Reviewed-on: https://gem5-review.googlesource.com/2720
Reviewed-by: Jason Lowe-Power <jason@lowepower.com>
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Change-Id: Iab5070fc9b666fcb5b49b0e2b99a4a1605b3b721
Signed-off-by: Andreas Sandberg <andreas.sandberg@arm.com>
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There is currently no good way of extracting the current operating
voltage in MathExprPowerModels. This change adds a magic variable,
'voltage', that can be referenced from such expressions to get the
current operating voltage.
Change-Id: Ice3c9a4a221921a542de5da52f83f3f88862d246
Signed-off-by: Andreas Sandberg <andreas.sandberg@arm.com>
Reviewed-by: Nikos Nikoleris <nikos.nikoleris@arm.com>
Reviewed-by: Sascha Bischoff <sascha.bischoff@arm.com>
Reviewed-on: https://gem5-review.googlesource.com/2662
Reviewed-by: Jason Lowe-Power <jason@lowepower.com>
Maintainer: Jason Lowe-Power <jason@lowepower.com>
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MathExprPower model currently doesn't print any useful error messages
if an expression fails to evaluate. To add insult to injury, the model
only detects a failure when dumping stats and not at
initialization. This change adds a verification step in startup() that
ensures that all of the referenced stats actually exist.
Change-Id: I8f71c73341578d5882c8d93e482f5383fbda5f1d
Signed-off-by: Andreas Sandberg <andreas.sandberg@arm.com>
Reviewed-by: Nikos Nikoleris <nikos.nikoleris@arm.com>
Reviewed-by: Sascha Bischoff <sascha.bischoff@arm.com>
Reviewed-on: https://gem5-review.googlesource.com/2661
Reviewed-by: Jason Lowe-Power <jason@lowepower.com>
Maintainer: Jason Lowe-Power <jason@lowepower.com>
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There are cases where Drainable objects need to create new objects in
Drainable::resume(). In such cases, the local drain state will be
inherited from the DrainManager. We currently set the state to Running
as soon as we start resuming the simulator. This means that new
objects are created in the Running state rather than the Drained
state, which the resume code assumes. Depending on the traversal order
in DrainManager::resume(), this sometimes triggers a panic because the
object being resumed is in the wrong state.
This change introduces a new drain state, Resuming, that the
DrainManager enters as soon as it starts resuming the
simulator. Objects that are created while resuming are created in this
state. Such objects are then resumed in a subsequent pass over the
list of Drainable objects that need to be resumed. Once all objects
have been resumed, the simulator enters the Running state.
Change-Id: Ieee8645351ffbdec477e9cd2ff86fc795e459617
Signed-off-by: Andreas Sandberg <andreas.sandberg@arm.com>
Reviewed-by: Curtis Dunham <curtis.dunham@arm.com>
Reviewed-on: https://gem5-review.googlesource.com/2600
Reviewed-by: Jason Lowe-Power <jason@lowepower.com>
Reviewed-by: Weiping Liao <weipingliao@google.com>
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The clone system call added in 236719892 relies on header files
from Linux systems. Obviously, this prevents compilation for
anyone using FreeBSD or Mac to compile the simulator. This
changeset is meant as a temporary fix to allow builds on
non-Linux systems until a proper solution is found.
Change-Id: I404cc41c588ed193dd2c1ca0c1aea35b0786fe4e
Reviewed-on: https://gem5-review.googlesource.com/2420
Maintainer: Brandon Potter <Brandon.Potter@amd.com>
Reviewed-by: Jason Lowe-Power <jason@lowepower.com>
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Change-Id: I9ff21092876593237f919e9f7fb7283bd865ba2e
Reviewed-on: https://gem5-review.googlesource.com/2421
Reviewed-by: Jason Lowe-Power <jason@lowepower.com>
Maintainer: Brandon Potter <Brandon.Potter@amd.com>
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Change-Id: I02719f3572f6665cace1eb5681f297dcde9e71ce
Reviewed-on: https://gem5-review.googlesource.com/2271
Reviewed-by: Andreas Sandberg <andreas.sandberg@arm.com>
Reviewed-by: Michael LeBeane <Michael.Lebeane@amd.com>
Reviewed-by: Tony Gutierrez <anthony.gutierrez@amd.com>
Maintainer: Jason Lowe-Power <jason@lowepower.com>
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The changeset does a major refactor on the exit, exit_group, and
futex system calls regarding exit functionality.
A FutexMap class and related structures are added into a new
file. This increases code clarity by encapsulating the futex
operations and the futex state into an object.
Several exit conditions were added to allow the simulator to end
processes under certain conditions. Also, the simulation only
exits now when all processes have finished executing.
Change-Id: I1ee244caa9b5586fe7375e5b9b50fd3959b9655e
Reviewed-on: https://gem5-review.googlesource.com/2269
Maintainer: Jason Lowe-Power <jason@lowepower.com>
Reviewed-by: Jason Lowe-Power <jason@lowepower.com>
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This changeset adds support to kill a thread group by calling
the tgkill system call. The functionality is needed in some
pthread applications.
Change-Id: I0413a3331be69b74dfab30de95384113ec4efb63
Reviewed-on: https://gem5-review.googlesource.com/2268
Maintainer: Jason Lowe-Power <jason@lowepower.com>
Reviewed-by: Tony Gutierrez <anthony.gutierrez@amd.com>
Reviewed-by: Michael LeBeane <Michael.Lebeane@amd.com>
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This changeset adds a simple class definition and a member
in the System object to track signals sent between processes.
The implementation cannot support all signals that might be
sent between processes, but it can support some of the simple
use cases like SIGCHLD.
Change-Id: Id5f95aa60e7f49da1c5b5596fbfa26e729453ac7
Reviewed-on: https://gem5-review.googlesource.com/2267
Reviewed-by: Michael LeBeane <Michael.Lebeane@amd.com>
Reviewed-by: Jason Lowe-Power <jason@lowepower.com>
Maintainer: Jason Lowe-Power <jason@lowepower.com>
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This changeset extends the pipe system call to work with
architectures other than Alpha (and enables the syscall for
x86). For the dup system call, it sets the clone-on-exec
flag by default. For the dup2 system call, the changeset
adds an implementation (and enables it for x86).
Change-Id: I00ddb416744ee7dd61a5cd02c4c3d97f30543878
Reviewed-on: https://gem5-review.googlesource.com/2266
Maintainer: Jason Lowe-Power <jason@lowepower.com>
Reviewed-by: Tony Gutierrez <anthony.gutierrez@amd.com>
Reviewed-by: Michael LeBeane <Michael.Lebeane@amd.com>
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This changeset adds refactors the existing open system call,
adds the openat variant (enabled for x86 builds), and adds
additional "special file" test cases for /proc/meminfo and
/etc/passwd.
Change-Id: I6f429db65bbf2a28ffa3fd12df518c2d0de49663
Reviewed-on: https://gem5-review.googlesource.com/2265
Maintainer: Jason Lowe-Power <jason@lowepower.com>
Reviewed-by: Tony Gutierrez <anthony.gutierrez@amd.com>
Reviewed-by: Michael LeBeane <Michael.Lebeane@amd.com>
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This changeset fixes line alignment issues, spacing, spelling,
etc. for files that are used during SE Mode.
Change-Id: Ie61b8d0eb4ebb5af554d72f1297808027833616e
Reviewed-on: https://gem5-review.googlesource.com/2264
Maintainer: Jason Lowe-Power <jason@lowepower.com>
Reviewed-by: Tony Gutierrez <anthony.gutierrez@amd.com>
Reviewed-by: Michael LeBeane <Michael.Lebeane@amd.com>
Reviewed-by: Andreas Sandberg <andreas.sandberg@arm.com>
Reviewed-by: Pierre-Yves Péneau <pierre-yves.peneau@lirmm.fr>
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The Process class is full of implementation details and
structures related to SE Mode. This changeset factors out an
internal class from Process and moves it into a separate file.
The purpose behind doing this is to clean up the code and make
it a bit more modular.
Change-Id: Ic6941a1657751e8d51d5b6b1dcc04f1195884280
Reviewed-on: https://gem5-review.googlesource.com/2263
Reviewed-by: Jason Lowe-Power <jason@lowepower.com>
Reviewed-by: Andreas Sandberg <andreas.sandberg@arm.com>
Maintainer: Andreas Sandberg <andreas.sandberg@arm.com>
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The Python wrappers get confused by the forward declarations in the
power framework. This changeset restructures the code slightly to
avoid the troublesome forward declarations.
Change-Id: Id8c93224f1988edb5fdf9d3abc6237f2f688c02d
Signed-off-by: Andreas Sandberg <andreas.sandberg@arm.com>
Reviewed-by: Andreas Hansson <andreas.hansson@arm.com>
Reviewed-by: Curtis Dunham <curtis.dunham@arm.com>
Reviewed-by: Sascha Bischoff <sascha.bischoff@arm.com>
Reviewed-on: https://gem5-review.googlesource.com/2227
Reviewed-by: Pierre-Yves Péneau <pierre-yves.peneau@lirmm.fr>
Reviewed-by: Jason Lowe-Power <jason@lowepower.com>
Maintainer: Jason Lowe-Power <jason@lowepower.com>
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The WaitRec structure in the Process class is unnecessary. There
is a member declaration inside of the Process class, waitList,
that uses the WaitRec definition. However, waitList is unused so
they are both dead bits of code. This changeset removes both the
WaitRec struct and waitList member from Process.
Change-Id: Ia6ee7488b9f47fd0f0ae29c818fba6ea0710699c
Reviewed-on: https://gem5-review.googlesource.com/2262
Reviewed-by: Tony Gutierrez <anthony.gutierrez@amd.com>
Reviewed-by: Michael LeBeane <Michael.Lebeane@amd.com>
Reviewed-by: Andreas Sandberg <andreas.sandberg@arm.com>
Maintainer: Jason Lowe-Power <jason@lowepower.com>
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simulations
Modifies the clone system call and adds execve system call. Requires allowing
processes to steal thread contexts from other processes in the same system
object and the ability to detach pieces of process state (such as MemState)
to allow dynamic sharing.
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This changeset add fields to the process object and adds the following
three system calls: setpgid, gettid, getpid.
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This changeset adds functionality that allows system calls to retry without
affecting thread context state such as the program counter or register values
for the associated thread context (when system calls return with a retry
fault).
This functionality is needed to solve problems with blocking system calls
in multi-process or multi-threaded simulations where information is passed
between processes/threads. Blocking system calls can cause deadlock because
the simulator itself is single threaded. There is only a single thread
servicing the event queue which can cause deadlock if the thread hits a
blocking system call instruction.
To illustrate the problem, consider two processes using the producer/consumer
sharing model. The processes can use file descriptors and the read and write
calls to pass information to one another. If the consumer calls the blocking
read system call before the producer has produced anything, the call will
block the event queue (while executing the system call instruction) and
deadlock the simulation.
The solution implemented in this changeset is to recognize that the system
calls will block and then generate a special retry fault. The fault will
be sent back up through the function call chain until it is exposed to the
cpu model's pipeline where the fault becomes visible. The fault will trigger
the cpu model to replay the instruction at a future tick where the call has
a chance to succeed without actually going into a blocking state.
In subsequent patches, we recognize that a syscall will block by calling a
non-blocking poll (from inside the system call implementation) and checking
for events. When events show up during the poll, it signifies that the call
would not have blocked and the syscall is allowed to proceed (calling an
underlying host system call if necessary). If no events are returned from the
poll, we generate the fault and try the instruction for the thread context
at a distant tick. Note that retrying every tick is not efficient.
As an aside, the simulator has some multi-threading support for the event
queue, but it is not used by default and needs work. Even if the event queue
was completely multi-threaded, meaning that there is a hardware thread on
the host servicing a single simulator thread contexts with a 1:1 mapping
between them, it's still possible to run into deadlock due to the event queue
barriers on quantum boundaries. The solution of replaying at a later tick
is the simplest solution and solves the problem generally.
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This changeset add spaces in a few spots and removes an unnecessary comment.
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This changeset adds the ability to set a close-on-exec flag for a given
file descriptor. It also reworks some of the logic surrounding setting and
retrieving flags from the file description.
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The traversal of drainable objects could potentially be
non-deterministic when using an unordered set containing object
pointers. To ensure that the iteration is deterministic, we switch to
a vector. Note that the lookup and traversal of the drainable objects
is not performance critical, so the change has no negative consequences.
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Several large changes happen in this patch.
The FDEntry class is rewritten so that file descriptors now correspond to
types: 'File' which is normal file-backed file with the file open on the
host machine, 'Pipe' which is a pipe that has been opened on the host machine,
and 'Device' which does not have an open file on the host yet acts as a pseudo
device with which to issue ioctls. Other types which might be added in the
future are directory entries and sockets (off the top of my head).
The FDArray class was create to hold most of the file descriptor handling
that was stuffed into the Process class. It uses shared pointers and
the std::array type to hold the FDEntries mentioned above.
The changes to these two classes needed to be propagated out to the rest
of the code so there were quite a few changes for that. Also, comments were
added where I thought they were needed to help others and extend our
DOxygen coverage.
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Moves aux_vector into its own .hh and .cc files just to get it out of the
already crowded Process files. Arguably, it could stay there, but it's
probably better just to move it and give it files.
The changeset looks ugly around the Process header file, but the goal here is
to move methods and members around so that they're not defined randomly
throughout the entire header file. I expect this is likely one of the reasons
why I several unused variables related to this class. So, the methods are
declared first followed by members. I've tried to aggregate them together
so that similar entries reside near one another.
There are other changes coming to this code so this is by no means the
final product.
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The numCpus method is misleading in that it's not really a measure of
how many CPUs might be executing a process, but how many thread contexts
are assigned to the process at any given point in time.
It's nice to highlight this distinction because thread contexts are never
reused in the same way that a CPU can be reused for multiple processes.
The reason that there is no reuse is that there is no CPU scheduler for SE.
The tru64 code intends to use this method and the accompanying contextIDs
field to support SMT and track the number of threads with some system calls.
With the up coming clone and exec patches, this paradigm must change. There
needs to be a 1:1 mapping between the thread contexts and processes so that
the process state between threads is allowed to vary when needed by Linux.
This should not break SMT for tru64 if the Process class is refactored so that
multiple Processes can share state between themselves. The following patches
will do the refactoring incrementally as features are added.
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It looks like tru64 has some nxm* system calls, but the two fields that
are defined in the Process class are unused by any of the code. There doesn't
appear to be any reference in the tru64 code.
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The EIOProcess class was removed recently and it was the only other class
which derived from Process. Since every Process invocation is also a
LiveProcess invocation, it makes sense to simplify the organization by
combining the fields from LiveProcess into Process.
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A KVM VM is typically a child of the System object already, but for
solving future issues with configuration graph resolution, the most
logical way to keep track of this object is for it to be an actual
parameter of the System object.
Change-Id: I965ded22203ff8667db9ca02de0042ff1c772220
Reviewed-by: Andreas Sandberg <andreas.sandberg@arm.com>
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Change-Id: Ifc65d42eebfd109c1c622c82c3c3b3e523819e85
Reviewed-by: Andreas Sandberg <andreas.sandberg@arm.com>
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The CxxConfigManager schould create objects by traversing the object tree
starting from the root object. However, currently objects are created in
aplphabetical order, which only works if the root object alphabetically
comes before any system object (e.g. 'root' < 'system'. Otherwise (e.g.
'a_system' < 'root'), object construction may fail. The reason for this
behaviour is, that the call to findObject() in the sorting code also
constructs the object if it is not yet existent. Then findTraversalOrder()
calls findObject("root") and subseqeuently calls findObject() on all the
children, and so on. However, the call to findTraversalOrder() is
redundant, since all objects are already created in alphabetical order.
This patch simply removes the alphabetical ordering, leading to the objects
being created starting from 'root'.
Reviewed at http://reviews.gem5.org/r/3778/
Signed-off-by: Jason Lowe-Power <jason@lowepower.com>
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Seeing build breakage after brandon@11801:
[ CXX] X86/sim/process.cc -> .o build/X86/sim/process.cc:137:64:
error: field '_pid' is uninitialized when used here
[-Werror,-Wuninitialized] static_cast<PageTableBase *>(new
ArchPageTable(name(), _pid, system)) : ^ build/X86/sim/process.cc:138:64:
error: field '_pid' is uninitialized when used here
[-Werror,-Wuninitialized] static_cast<PageTableBase *>(new
FuncPageTable(name(), _pid))), ^ 2 errors generated.
Testing Done: Compiles now on FreeBSD 10 with clang.
Reviewed at http://reviews.gem5.org/r/3804/
Signed-off-by: Jason Lowe-Power <jason@lowepower.com>
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See developers mailing list. Trying to unbreak statfs.
Testing Done:
Builds on FreeBSD now.
Reviewed at http://reviews.gem5.org/r/3803/
Signed-off-by: Jason Lowe-Power <jason@lowepower.com>
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Python's header files set various compiler macros (e.g.,
_XOPEN_SOURCE) unconditionally. This triggers preprocessor warnings
that end up being treated as errors. The Python integration manual [1]
strongly recommends that Python.h is included before any system
header. The style guide used to mandate that Python.h is included
first in any file that needs it. This requirement was changed to
always include a source file's main header first, which ended up
triggering these errors.
This change updates the style checker to always include Python.h
before the main header file.
[1] https://docs.python.org/2/extending/extending.html
Change-Id: Id6a4f7fc64a336a8fd26691a0ca682abeb1d1579
Signed-off-by: Andreas Sandberg <andreas.sandberg@arm.com>
Reviewed-by: Nikos Nikoleris <nikos.nikoleris@arm.com>
Reviewed-by: Jason Lowe-Power <jason@lowepower.com>
Reviewed-by: Pierre-Yves Péneau <pierre-yves.peneau@lirmm.fr>
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Used cppclean to help identify useless includes and removed them. This
involved erroneously included headers, but also cases where forward
declarations could have been used rather than a full include.
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The class was crammed into syscall_emul.hh which has tons of forward
declarations and template definitions. To clean it up a bit, moved the
class into separate files and commented the class with doxygen style
comments. Also, provided some encapsulation by adding some accessors and
a mutator.
The syscallreturn.hh file was renamed syscall_return.hh to make it consistent
with other similarly named files in the src/sim directory.
The DPRINTF_SYSCALL macro was moved into its own header file with the
include the Base and Verbose flags as well.
--HG--
rename : src/sim/syscallreturn.hh => src/sim/syscall_return.hh
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The CountedDrainEvent event was used to keep track of objects that
required additional simulation to drain. It was removed as a part of
the great drain rewrite, but the declaration remained.
Change-Id: I767a3213669040d3f27e2afafa2e4a5bb997e325
Signed-off-by: Andreas Sandberg <andreas.sandberg@arm.com>
Reviewed-by: Curtis Dunham <curtis.dunham@arm.com>
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The headers declared in export_method_cxx_predecls are redundant since a
SimObject's main header is automatically included.
Change-Id: Ied9e84630b36960e54efe91d16f8c66fba7e0da0
Signed-off-by: Andreas Sandberg <andreas.sandberg@arm.com>
Reviewed-by: Curtis Dunham <curtis.dunham@arm.com>
Reviewed-by: Joe Gross <joseph.gross@amd.com>
Reviewed-by: Jason Lowe-Power <jason@lowepower.com>
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When restoring from a checkpoint, the simulation used to use file handles from
the checkpoint. This disallows multiple separate restore simulations from using
separate input and output files and directories, and plays havoc when the
checkpointed file locations may have changed. Add handling to allow the command
line specified files to be used as input/output for the restored simulation
(Note: this is the similar functionality to FS mode for output and error).
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