Logging and Diagnostics


This section provides reference information on the use of the diagnostic stream classes. For an overview of the diagnostic stream concepts refer to the introductory chapter.

Working with Diagnostic Streams (*)

The CNcbiDiag class implements the functionality of an output stream enhanced with error posting mechanisms similar to those found in the NCBI C Toolkit. A CNcbiDiag object has the look and feel of an output stream; its member functions and friends include output operators and format manipulators. A CNcbiDiag object is not itself a stream, but serves as an interface to a stream which allows multiple threads to write to the same output. Each instance of CNcbiDiag includes the following private data members:

  • a buffer to store (a single) message text

  • a severity level

  • a set of post flags

Limiting each instance of CNcbiDiag to the storage and handling of a single message ensures that multiple threads writing to the same stream will not have interleaving message texts.

The following topics are discussed in this section:

Where Diagnostic Messages Go

The following decision tree describes how the destination for diagnostics messages is determined.

  1. Before the application is constructed (before AppMain() is called), everything goes to:

    1. (Unix-like systems only) /log/fallback/UNKNOWN.{log|err|trace} – if available

    2. STDERR – otherwise

  2. When the application is ready, and its name is known, but before the configuration file is loaded:

    1. If AppMain() is passed flags eDS_Default or eDS_ToStdlog, then the diagnostics goes:

      1. (Unix-like systems only) if /log is present:

        1. if the application is described in /etc/toolkitrc – to /log/<token>/appname.{log|err|trace}

        2. else if environment variable $SERVER_PORT is set – to /log/$SERVER_PORT/appname.{log|err|trace}

        3. else (or if failed to switch to one of the above two locations) – to /log/srv/appname.{log|err|trace}

        4. or, if failed to switch to that – to /log/fallback/appname.{ log|err|trace}

      2. else (or if failed to switch to any of the /log location):

        1. eDS_ToStdlog – to <current_working_dir>/appname.{ log|err|trace} (and, if cannot, then continues to go to STDERR)

        2. eDS_Default – continues to go to STDERR

    2. If AppMain() is passed flags other than eDS_Default or eDS_ToStdlog, then the diagnostics goes to:

      1. eDS_ToStdout – standard output stream

      2. eDS_ToStderr – standard error stream

      3. eDS_ToMemory – the application memory

      4. eDS_Disable – nowhere

      5. eDS_User – wherever it went before the AppMain() call

      6. eDS_ToSyslog – system log daemon

  3. After the configuration file is loaded, and if it has an alternative location for the log files, then switch to logging to that location. See the list of logfile-related configuration parameters.

The boolean TryRootLogFirst argument in the [LOG] section of the application’s config file changes the order of locations to be tested. If TryRootLogFirst is set, the application will try to open the log file under /log first. Only if this fails, then the location specified in the config file will be used.


  • If the logging destination is switched, then a message containing both the old and new locations is logged to both locations.

  • Before the application configuration is loaded, a copy of all diagnostics is saved in memory. If the log destination is changed by the application configuration, then the saved diagnostics are dumped to the final log destination.

Setting Diagnostic Severity Levels

Each diagnostic message has its own severity level (EDiagSev), which is compared to a global severity threshold to determine whether or not its message should be posted. Six levels of severity are defined by the EDiagSev enumeration:

/// Severity level for the posted diagnostics.
enum EDiagSev {
    eDiag_Info = 0, ///< Informational message
    eDiag_Warning,  ///< Warning message
    eDiag_Error,    ///< Error message
    eDiag_Critical, ///< Critical error message
    eDiag_Fatal,    ///< Fatal error -- guarantees exit(or abort)
    eDiag_Trace,    ///< Trace message

Please note that eDiag_Trace is a value of EDiagSev for historical reasons. It is NOT treated as a severity level. It is a separate entity that is just a part of enum EDiagSev.

The default is to post only those messages whose severity level exceeds the eDiag_Warning level (i.e. eDiag_Error, eDiag_Critical, and eDiag_Fatal). The global severity threshold for posting messages can be reset using SetDiagPostLevel (EDiagSev postSev). A parallel function, SetDiagDieLevel (EDiagSev dieSev), defines the severity level at which execution will abort.

Tracing is considered to be a special, debug-oriented feature, and therefore messages with severity level eDiag_Trace are not affected by these global post/die levels. Instead, SetDiagTrace (EDiagTrace enable, EDiagTrace default) is used to turn tracing on or off. By default, the tracing is off - unless you assign the environment variable DIAG_TRACE to an arbitrary non-empty string or, alternatively, define a DIAG_TRACE entry in the [DEBUG] section of your registry file.

The severity level can be set directly in POST and TRACE statements, using the severity level manipulators including Info, Warning, Error, Critical, Fatal, and Trace, for example:

ERR_POST_X(1, Critical << "Something quite bad has happened.");

Diagnostic Messages Filtering

Diagnostic messages from the CNcbiDiag and CException classes can be filtered by the source file path; message severity; or by the module, class, or function name. Messages from the CNcbiDiag class can also be filtered by error code. If a CException object is created by chaining to a previous exception, then all exceptions in the chain will be checked against the filter and the exception will pass if any exception in the chain passes (even if one of them is suppressed by a negative condition).

The filter can be set by the TRACE_FILTER or POST_FILTER entry in the [DIAG] section of the registry file or during runtime through SetDiagFilter(). Messages with a severity level of Fatal are not filtered; messages with a severity level of Trace are filtered by TRACE_FILTER; and all other messages are filtered by POST_FILTER.

Filter strings contain filtering conditions separated by a space. An empty filter string means that all messages will appear in the log unfiltered. Filtering conditions are processed from left to right until a condition that matches the message is found. If the message does not match any of the conditions, then the message will be filtered out. Filtering conditions in the string may be preceded by an exclamation mark, which reverses the behavior (so if a message matches the condition it will be suppressed). See Table 4 for filtering condition samples and syntax.

Table 4. Filter String Samples

Filter Description Matches Non Matches
/corelib Log message from source file located in src/corelib or include/corelib or subdirectories.
  • src/corelib/ncbidiag.cpp

  • src/corelib/test/test_ncbiexec.cpp

  • include/corelib/ncbidiag.hpp

  • src/cgi/cgiapp.cpp

/corelib/test Log message from source file located in src/corelib/test or include/corelib/test or subdirectories.
  • src/corelib/test/test_ncbiexec.cpp

  • src/corelib/ncbidiag.cpp

  • include/corelib/ncbidiag.hpp

  • src/cgi/cgiapp.cpp

/corelib/ Log message from source file located in src/corelib or include/corelib, but not subdirectories.
  • src/corelib/ncbidiag.cpp

  • include/corelib/ncbidiag.hpp

  • src/corelib/test/test_ncbiexec.cpp

  • src/cgi/cgiapp.cpp

corelib Log message with module name set to "corelib" and any class or function name.
  • corelib

  • corelib::CNcbiDiag

  • corelib::CNcbiDiag::GetModule()

  • CNcbiDiag

  • CNcbiDiag::GetModule()

  • GetModule()

corelib::CNcbiDiag Log message with module name set to "corelib", class name set to "CNcbiDiag" and any function name.
  • corelib::CNcbiDiag

  • corelib::CNcbiDiag::GetModule()

  • corelib

  • CNcbiDiag

  • CNcbiDiag::GetModule()

  • GetModule()

::CNcbiDiag Log message with class name set to "CNcbiDiag" and any module or function name.
  • corelib::CNcbiDiag

  • corelib::CNcbiDiag::GetModule()

  • CNcbiDiag

  • CNcbiDiag::GetModule()

  • corelib

  • GetModule()

? Log message with module name not set and any class or function name.
  • CNcbiDiag

  • CNcbiDiag::GetModule()

  • GetModule()

  • corelib

  • corelib::CNcbiDiag

  • corelib::CNcbiDiag::GetModule()

  • corelib::CNcbiDiag::GetModule()

corelib::? Log message with module name set to "corelib", class name not set and any function name.
  • corelib

  • corelib::GetModule()

  • corelib::CNcbiDiag

  • corelib::CNcbiDiag::GetModule()

  • CNcbiDiag::GetModule()

  • GetModule()

GetModule() Log message with function name set to "GetModule" and any class or module name.
  • corelib::GetModule()

  • CNcbiDiag::GetModule()

  • GetModule()

  • Corelib

  • corelib::CNcbiDiag

  • CNcbiDiag

(20.11) Log messages with error code 20 and subcode 11.
  • ErrCode(20,11)

  • ErrCode(20,10)

  • ErrCode(123,11)

(20-80.) Log messages with error code from 20 to 80 and any subcode.
  • ErrCode(20,11)

  • ErrCode(20,10)

  • ErrCode(51,1)

  • ErrCode(123,11)

(20-80,120,311-400.1-50,60) Log messages with error code from 20 to 80, 120, from 311 to 400 and subcode from 1 to 50 and 60.
  • ErrCode(20,11)

  • ErrCode(321,60)

  • ErrCode(20,51)

  • ErrCode(321,61)

For example:

  • To log diagnostic messages from source files located in src/corelib with error codes from 101 to 106 and any subcode, use the following filter: “/corelib (101-106.)”.

  • To exclude log messages from sources in src/serial and src/dbapi, use this filter: “!/serial !/dbapi”.

  • To log messages from sources in src/serial excluding those with error code 802 and subcodes 4 and 10 through 12, and to exclude messages from sources in src/dbapi/driver, use the following filter: “/serial !(802.4,10-12) !/dbapi/driver”.

Log File Format

The format of the log file can be customized. One of the most basic choices is between the “old post format” and the “new post format”. The old format essentially posts arbitrary strings whereas the new format adds many standard fields, and structures the messages so they can be automatically indexed for rapid searching and/or error statistics.

The old format is used by default. To use the new format:

int main(int argc, const char* argv[])
    GetDiagContext().SetOldPostFormat(false); // use the new format

    return CMyApp().AppMain(argc, argv);

This function should be called before the application’s constructor for the setting to be used from the very beginning.

See also:

  • the Diagnostic Trace section in the library configuration chapter for details on selecting the format using the environment or registry; and

  • the ERR_POST and LOG_POST Macros section for more details on creating the log messages.

Note: The old and new post formats described below apply to log messages generated by programs using the C++ Toolkit diagnostics API. Log messages generated in other ways may have different formats.

The Old Post Format

The old format for log messages is simply a message - prefixed with the severity level if it is an error message:

[<severity>: ]<Message>

The New Post Format

A log file using new format is a binary file containing messages separated with line feed characters (\n, 0x0A). Messages are composed of several predefined fields, each field may contain binary content. To prevent line feeds from appearing in a message body it is encoded using the following table:

Original byte Encoded sequence
0x0A (\n) 0x0B (\v)
0x0B 0xFF 0x0B
0xFF 0xFF 0xFF


On some platforms if log output is sent to a text stream (e.g. console) the message separator may be replaced with the platform specific newline character or sequence.

The new format for the application log and error postings is:

<pid>/<tid>/<rid>/<state> <guid> <psn>/<tsn> <time> <host> <client> <session> <application> <event> <message>

Fields in the new post format:

Field Description Width Type or format
pid Process ID ≥ 5 Uint8 (decimal)
tid Thread ID ≥ 3 Uint8 (decimal)
rid Request ID (e.g. iteration number for a CGI) ≥ 4 int (decimal)
state Application state code 2 string
guid Globally unique process ID 16 Int8 (hexadecimal)
psn Serial number of the posting within the process ≥ 4 int (decimal)
tsn Serial number of the posting within the thread ≥ 4 int (decimal)
time Astronomical date and time at which the message was posted ≥ 23
(often 26)
While seconds typically have six digits after the decimal, there could be more or as few as three.
host Name of the host where the process runs 15 string (UNK_HOST if unknown)
client Client IP address 15 valid IP address string (UNK_CLIENT if unknown)
session Session ID ≥ 24 string (UNK_SESSION if unknown)
application Name of the application (see note below) varies string (UNK_APP if unknown)
event What was happening to cause the post (e.g. app start) 13 string (see the Events and Messages section)
message The logged message varies string (see the Events and Messages section)

Note: Regarding the width and padding of standard fields:

  • Minimum-width numeric fields are right-justified and zero-padded - for example, a pid of 123 will get printed as “00123” while a pid of 1234567 will get printed as “1234567”.

  • Minimum-width text fields and fixed-width fields are left-justified and space-padded.

  • Most fields have a fixed or minimum width to improve readability by generally aligning fields in adjacent rows.

The application name is set to the executable name (without path and extension) by default. Sometimes however the executable’s name can be too generic (like “summary” or “fetch”). To change it use CNcbiApplication::SetProgramDisplayName() function. Better yet, just rename the executable itself. It’s a good practice to prefix the application names with something project-specific (like “pc_summary” for PubChem or “efetch” for E-Utils).

For more details, see:

Application States

Application state codes:

Application State Code Meaning
PB (or AB) program is starting
P (or A) program is running (outside of any request)
PE (or AE) program is exiting
RB request is starting
R request is being processed
RE request is exiting

Note: The “A” and “P” codes are essentially synonymous. The “P” codes are generated by newer programs, but the “A” codes may still be present in some data.

The normal state transitions are:

Image ch_core_log_fmt_app_states.png

Events and Messages

The following sections describe the events and messages seen in the log files:

Event: The application starts

The <event> <message> portion of the log output will contain:


(The message field is empty for the start event.)

Event: The application stops

The <event> <message> portion of the log output will contain:

stop <exit_code> <timespan> [SIG=<exit_signal>]

Application stop event - message sub-fields:

Sub-field Description
exit_code Application exit code (zero if not set)
timespan Application execution time (in seconds; floating-point)
exit_signal Signal number, if application exited due to a signal

For example:

stop            0 0.149036509

Event: A request starts

The <event> <message> portion of the log output will contain:

request-start [application_defined_data]

The message field for the request-start event optionally contains application-specific arbitrary data, for example:

request-start _type=conn

Note: Make your log data more parsable!

Although the request-start data may be arbitrary, it should be URL-encoded. In many cases the logs are collected and stored in the database for analysis. The NCBI log system now parses and indexes the application-supplied data in the request-start and extra log lines, provided that the data is URL-encoded.

Event: The application posts extra information (within the context of a request)

The <event> <message> portion of the log output will contain:

extra <application_defined_data>

The message field for the extra event has the same format as the message field for the request-start event.

Event: A request stops

The <event> <message> portion of the log output will contain:

request-stop <status> <req_timespan> [bytes_read] [bytes_written]

The message sub-fields for request-stop events are:

Request stop event - message sub-fields:

Sub-field Description
status Exit status of the request (zero if not set)
req_timespan Request execution time (zero if not set; in seconds, floating-point)
bytes_read Input data read during the request execution, in bytes (zero if not set)
bytes_written Output data written during the request execution, in bytes (zero if not set)

For example:

request-stop  200 0.105005566

Event: The application posts a diagnostic message

The <event> <message> portion of the log output will contain:

<severity>: <module>(<err_code>.<err_subcode> | <err_text>) "<file>", line <line>: <class>::<func> --- <prefixes> <user_message> <err_code_message> <err_code_explanation>

Thus, the <event> field is really just the diagnostic message severity, and the <message> field is composed of a number of sub-fields.

Diagnostic message event / severity field - message sub-fields:

Field or sub-field Description
event / severity Diagnostic message severity = { Trace | Info | Warning | Error | Critical | Fatal | Note[T|I|W|E|C|F] } - left-justified and space-padded to 10 characters
module Module where the post originates from (in most cases the module corresponds to a single library)
err_code, err_subcode Numeric error code and subcode
err_text If the error has no numeric code, sometimes it can be represented as text
file, line File name and line number where the posting occured
class, func Class and/or function name where the posting occured: {Class:: | Class::Function() | ::Function()}
prefixes User-defined prefixes for the message
user_message The message itself
err_code_message Short error code description
err_code_explanation Detailed explanation of the error code

Event: The application posts performance logging information

The <event> <message> portion of the log output will contain:

perf <exit_code> <timespan> <performance_parameters>

The message sub-fields for perf events are:

Performance logging event - message sub-fields:

Sub-field Description
exit_code Application exit code (zero if not set)
timespan Application execution time
performance_parameters URL-encoded name=value pairs – the resource name given to the logger, the status message (if given), and any others from AddParameter()

For example:

perf            200 0.000246 resource=task+one&status_msg=task+one+finished


An example of application events:

Image ch_core_log_fmt_event.png

(Click to see the full-resolution image.)

An example of diagnostic messages:

Image ch_core_log_fmt_diagnostic.png

(Click to see the full-resolution image.)

Controlling the Appearance of Diagnostic Messages using Post Flags

The post flags define additional information that will be inserted into the output messages and appear along with the message body. The standard format of a message is:

"<file>", line <line>: <severity>: (<err_code>.<err_subcode>) [<prefix1>::<prefix2>::<prefixN>] <message>\n

where the presence of each field in the output is controlled by the post flags EDiagPostFlag associated with the particular diagnostic message. The post flags are:

enum EDiagPostFlag {
    eDPF_File               = 0x1, ///< Set by default #if _DEBUG; else not set
    eDPF_LongFilename       = 0x2, ///< Set by default #if _DEBUG; else not set
    eDPF_Line               = 0x4, ///< Set by default #if _DEBUG; else not set
    eDPF_Prefix             = 0x8, ///< Set by default (always)
    eDPF_Severity           = 0x10,  ///< Set by default (always)
    eDPF_ErrorID            = 0x20,  ///< Module, error code and subcode
    eDPF_DateTime           = 0x80,  ///< Include date and time
    eDPF_ErrCodeMessage     = 0x100, ///< Set by default (always)
    eDPF_ErrCodeExplanation = 0x200, ///< Set by default (always)
    eDPF_ErrCodeUseSeverity = 0x400, ///< Set by default (always)
    eDPF_Location           = 0x800, ///< Include class and function
                                     ///< if any, not set by default
    eDPF_PID                = 0x1000,  ///< Process ID
    eDPF_TID                = 0x2000,  ///< Thread ID
    eDPF_SerialNo           = 0x4000,  ///< Serial # of the post, process-wide
    eDPF_SerialNo_Thread    = 0x8000,  ///< Serial # of the post, in the thread
    eDPF_RequestId          = 0x10000, ///< fcgi iteration number or request ID
    eDPF_Iteration          = 0x10000, ///< @deprecated
    eDPF_UID                = 0x20000, ///< UID of the log

    eDPF_ErrCode            = eDPF_ErrorID,  ///< @deprecated
    eDPF_ErrSubCode         = eDPF_ErrorID,  ///< @deprecated
    /// All flags (except for the "unusual" ones!)
    eDPF_All                = 0xFFFFF,

    /// Default flags to use when tracing.
#if defined(NCBI_THREADS)
    eDPF_Trace              = 0xF81F,
    eDPF_Trace              = 0x581F,

    /// Print the posted message only; without severity, location, prefix, etc.
    eDPF_Log                = 0x0,

    // "Unusual" flags -- not included in "eDPF_All"
    eDPF_PreMergeLines      = 0x100000, ///< Remove EOLs before calling handler
    eDPF_MergeLines         = 0x200000, ///< Ask diag.handlers to remove EOLs
    eDPF_OmitInfoSev        = 0x400000, ///< No sev. indication if eDiag_Info
    eDPF_OmitSeparator      = 0x800000, ///< No '---' separator before message

    eDPF_AppLog             = 0x1000000, ///< Post message to application log
    eDPF_IsMessage          = 0x2000000, ///< Print "Message" severity name.

    /// Hint for the current handler to make message output as atomic as
    /// possible (e.g. for stream and file handlers).
    eDPF_AtomicWrite        = 0x4000000,

    /// Use global default flags (merge with).
    /// @sa SetDiagPostFlag(), UnsetDiagPostFlag(), IsSetDiagPostFlag()
    eDPF_Default            = 0x10000000,

    /// Important bits which should be taken from the globally set flags
    /// even if a user attempts to override (or forgets to set) them
    /// when calling CNcbiDiag().
    eDPF_ImportantFlagsMask = eDPF_PreMergeLines |
                              eDPF_MergeLines |
                              eDPF_OmitInfoSev |
                              eDPF_OmitSeparator |

    /// Use flags provided by user as-is, do not allow CNcbiDiag to replace
    /// "important" flags by the globally set ones.
    eDPF_UseExactUserFlags  = 0x20000000

The default message format displays only the severity level and the message body. This can be overridden inside the constructor for a specific message, or globally, using SetDiagPostFlag() on a selected flag. For example:

    SetDiagPostFlag(eDPF_DateTime); // set flag globally

Defining the Output Stream

The logging framework uses a global output stream. The default is to post messages to CERR ouput stream, but the stream destination can be reset at any time using:

SetDiagStream(CNcbiOstream* os, bool quick_flush,
              FDiagCleanup cleanup, void* cleanup_data)

This function can be called numerous times, thus allowing different sections of the executable to write to different files. At any given time however, all messages will be associated with the same global output stream. Because the messages are completely buffered, each message will appear on whatever stream is active at the time the message actually completes.

And, of course, you can provide (using SetDiagHandler) your own message posting handler CDiagHandler, which does not necessarily write the messages to a standard C++ output stream. To preserve compatibility with old code, SetDiagHandler also continues to accept raw callback functions of type FDiagHandler.

If the output is sent to a file, you can split it into separate files:

  • Application log - standard events (start, stop, request-start, request-stop and user defined extra events).

  • Error log - all messages with severity Warning and above.

  • Trace log - messages having severity Info and Trace messages.

  • Performance log - messages from performance logging.

All log files have the same name but different extensions: .log, .err, .trace, and .perf.

To turn on the log file splitting, call (before the log file initialization):

int main(int argc, const char* argv[])

    return CMyApp().AppMain(argc, argv);

This function should be called before the application’s constructor for the setting to be used from the very beginning.

Tee Output to STDERR

Sometimes it is helpful to generate human-readable diagnostics on the console in addition to storing detailed diagnostics in the machine-parsable log files. In these cases, it is likely that both the message severity required to trigger output and the output format should be different for the log file and the console. For example:

Destination Severity Format
Log File Error new (machine-parsable)
Console Warning old (human-readable)

To set up this sort of tee, set these configuration parameters (see the library configuration chapter for details):

Configuration Parameter Example Value Notes
DIAG_TEE_TO_STDERR True This turns on the tee.
DIAG_OLD_POST_FORMAT False This makes the log file use the new format.
DIAG_POST_LEVEL Error This sets the minimum severity required to post to the log file.
DIAG_TEE_MIN_SEVERITY Warning This sets the minimum severity required to post to the console.

Alternatively, you can use the Console manipulator to indicate that output should go to the console (in human-readable format):

ERR_POST_X(1, Console << "My ERR_POST message.");

Note: Output sent to the console using this manipulator will also go to the log file if the message severity at least meets the severity threshold for the log file. The effect of the manipulator lasts until the next flush, which typically occurs after each post.

The Message Buffer

Diagnostic messages (i.e. instances of the CNcbiDiag class) have a buffer that is initialized when the message is first instantiated. Additional information can then be appended to the message using the overloaded stream operator <<. Messages can then be terminated explicitly using CNcbiDiag’s stream manipulator Endm, or implicitly, when the CNcbiDiag object exits scope.

Implicit message termination also occurs as a side effect of applying one of the severity level manipulators. Whenever the severity level is changed, CNcbiDiag also automatically executes the following two manipulators:

  • Endm – the message is complete and the message buffer will be flushed

  • Reset – empty the contents of the current message buffer

When the message controlled by an instance of CNcbiDiag is complete, CNcbiDiag calls a global callback function (of type FDiagHandler) and passes the message (along with its severity level) as the function arguments. The default callback function posts errors to the currently designated output stream, with the action (continue or abort) determined by the severity level of the message.

Logging Requests

In request-driven applications (like FastCGIs or CServer-based) grouping diagnostics into request-specific blocks is very helpful for post-processing. To facilitate this, CDiagContext provides the PrintRequestStart(), PrintRequestStop(), Extra(), and various Print(), methods.

The CDiagContext::SetRequestContext() method enables you to use a CRequestContext object to pass certain request-specific information - such as request ID, client IP, bytes sent, request status, etc. - to the diagnostics context. The request context information can be invaluable when analyzing logs.

CRequestContext objects are merely convenient packages for passing information - they can be preserved across multiple events or re-created as needed. However, as CObject-derived objects, they should be wrapped by CRef to avoid inadvertent deletion by code accepting a CRef parameter.

The following code fragments show examples of API calls for creating request-specific blocks in the logfile. Your code may be slightly different and may make these calls in different event handlers (for example, you might call PrintRequestStart() in OnRead() and PrintRequestStop() in OnWrite()).

// Set up the request context:
CRef<CRequestContext> rqst_ctx(new CRequestContext());

// Access the diagnostics context:
CDiagContext & diag_ctx(GetDiagContext());

// Start the request block in the log:
        .Print("peer", "")
        .Print("port", 5555);

// Other relevant info...
CDiagContext_Extra extra(diag_ctx.Extra());
extra.Print("name1", "value1")
     .Print("name2", "value2");

// Terminate the request block in the log.

Code like the above will result in AppLog entries that look similar to:

Image ch_grid_cserver_applog.png

Each thread has its own request context. Therefore, simultaneous calls to GetDiagContext().SetRequestContext() in multiple event handlers will not interfere with each other. If GetDiagContext().SetRequestContext() is not called (or is called with NULL argument), the default request context, also unique to each thread, is used.

It is possible to pass request context from one thread to another. In this case the context must be removed from the old thread before passing it to GetDiagContext().SetRequestContext() in the new thread.

The request handler should ensure that each request-start has a corresponding request-stop - for example by writing the request-stop in a destructor if it wasn’t already written. PrintRequestStop() resets request context’s properties so that a new request does not inherit any information from the previous request.

Using subhit IDs to express call tree hierarchy

See here.

Request Exit Status Codes

This section describes the possible values of the request exit codes used in NCBI. They appear in the application access log as:

request-stop <status> .....

Request exit status codes are either standard or NCBI-specific.

Standard (HTTP-like) status codes

The NCBI request exit codes must conform to the HTTP status codes:

NCBI-specific status codes

If the situation cannot be described using one of the standard (HTTP) status codes, then an NCBI specific code should be used.

The NCBI-specific status codes must be different from the standard (HTTP) status codes. At the same time these codes better follow at least the range requirements of the standard (HTTP) status codes, that is they better belong to one of the following ranges:

Range Description
120 – 199 Informational/provisional response
220 – 299 Success
320 – 399 Redirection
420 – 499 Bad request (client error)
520 – 599 Server Error

So far we have the following NCBI specific status codes:

Value Description
0 Unknown error
299 Broken connection while serving partial-content request (usually expected)
499 Broken connection while serving regular request (usually unexpected, indicates n/w, communication protocol or cliend-side problem)
555 NCBI Network Dispatcher refused a request from and outside user which is in its “abusers list”
1000 + errno Unclassifiable server error when only errno is known (NOTE: the value of errno can be different on different platforms!)

Error codes and their Descriptions

Error codes and subcodes are posted to an output stream only if applicable post flags were set. In addition to error codes, the logging framework can also post text explanations. The CDiagErrCodeInfo class is used to find the error message that corresponds to a given error code/subcode. Such descriptions could be specified directly in the program code or placed in a separate message file. It is even possible to use several such files simultaneously. CDiagErrCodeInfo can also read error descriptions from any input stream(s), not necessarily files.

Preparing an Error Message File

The error message file contains plain ASCII text data. We would suggest using the .msg extension, but this is not mandatory. For example, the message file for an application named SomeApp might be called SomeApp.msg.

The message file must contain a line with the keyword MODULE in it, followed by the name of the module (in our example SomeApp). This line must be placed in the beginning of the file, before any other declarations. Lines with symbol # in the first position are treated as comments and ignored.

Here is an example of the message file:

# This is a message file for application "SomeApp"
# ------ Code 1 ------
$$ NoMemory, 1, Fatal : Memory allocation error
# ------ Code 2 ------
$$ File, 2, Critical : File error
$^ Open, 1 : Error open a specified file
This often indicates that the file simply does not exist.
Or, it may exist but you do not have permission to access
the file in the requested mode.
$^ Read, 2, Error : Error read file
Not sure what would cause this...
$^ Write, 3, Critical
This may indicate that the filesystem is full.
# ------ Code 3 ------
$$ Math, 3
$^ Param, 20
$^ Range, 3

Lines beginning with $$ define a top-level error code. Similarly, lines beginning with $^ define subcodes of the top-level error code. In the above example Open is a subcode of File top-level error, which means the error with code 2 and subcode 1.

Both types of lines have similar structure:

$$/$^ <mnemonic_name>, <code> [, <severity> ] [: <message> ] \n
[ <explanation> ]


  • mnemonic_name (required) Internal name of the error code/subcode. This is used as a part of an error name in a program code - so, it should also be a correct C/C++ identifier.

  • code (required) Integer identifier of the error.

  • severity (optional) This may be supplied to specify the severity level of the error. It may be specified as a severity level string (valid values are Info, Warning, Error, Critical, Fatal, Trace) or as an integer in the range from 0 (Info) to 5 (Trace). While integer values are acceptable, string values are more readable. If the severity level was not specified or could not be recognized, it is ignored, or inherited from a higher level (the severity of a subcode becomes the same as the severity of a top-level error code, which contains this subcode). As long as diagnostic eDPF_ErrCodeUseSeverity flag is set, the severity level specified in the message file overrides the one specified in a program, which allows for runtime customization. In the above example, Critical severity level will be used for all File errors, except Read subcode, which would have Error severity level.

  • message (optional) Short description of the error. It must be a single-line message. As long as diagnostic eDPF_ErrCodeMessage flag is set, this message is posted as a part of the diagnostic output.

  • explanation (optional) Following a top-level error code or a subcode definition string, it may be one or several lines of an explanation text. Its purpose is to provide additional information, which could be more detailed description of the error, or possible reasons of the problem. This text is posted in a diagnostic channel only if eDPF_ErrCodeExplanaton flag was set.

Error message files can be automatically read by setting a configuration parameter. You can either define the MessageFile entry in the DEBUG section of the application registry, or set the environment variable NCBI_CONFIG__DEBUG__MessageFile (note the double-underscores and character case).

Defining Custom Handlers using CDiagHandler

The user can install his own handler (of type CDiagHandler,) using SetDiagHandler(). CDiagHandler is a simple abstract class:

class  CDiagHandler
    /// Destructor.
    virtual ~CDiagHandler(void) {}
    /// Post message to handler.
    virtual void Post(const SDiagMessage& mess) = 0;

where SDiagMessage is a simple struct defined in ncbidiag.hpp whose data members’ values are obtained from the CNcbiDiag object. The transfer of data values occurs at the time that Post is invoked. See also the section on Message posting for a more technical discussion.

The ERR_POST and LOG_POST Macros

A family of ERR_POST* macros and a corresponding family of LOG_POST* macros are available for routine message posting.

The log entries produced by the two families are almost identical for the new post format - the ERR_POST* entries contain a full word for the severity (e.g. “Error”) while the LOG_POST* entries contain the word “Note” and a one-character severity code (e.g. “Note[E]”). For the old post format, LOG_POST* macros simply contain the message, while ERR_POST* entries contain the severity, error code, and message. Message filtering works exactly the same way for the two families of macros.

Note that the the “Note” messages (from LOG_POST*) do not show by default in the AppLog browser. You need to check the “Note” checkbox to see them.

The macros are:

  • {ERR|LOG}_POST(msg) – for posting a simple message. Note: these macros are deprecated. Use {ERR|LOG}_POST_X instead (except for tests) for more flexible error statistics and logging.

  • {ERR|LOG}_POST_X(subcode, msg) – for posting a default error code, a given subcode, and a message. Each call to {ERR|LOG}_POST_X must use a different subcode for proper error statistics and logging. The default error code is selected by NCBI_USE_ERRCODE_X. The error code is selected from those defined by NCBI_DEFINE_ERRCODE_X in the appropriate header file, e.g. include/corelib/error_codes.h.

  • {ERR|LOG}_POST_EX(code, subcode, msg) – for posting a given error code, a given error subcode, and a message. This macro should only be used if you have to use a variable for the subcode, or to specify an error code other than the current default. In all other cases (except for tests), use {ERR|LOG}_POST_X for more flexible error statistics and logging.

  • {ERR|LOG}_POST_XX(code, subcode, msg) – these macros must be used in place of {ERR|LOG}_POST_X within header files so that the same error code will be used for header-defined code, regardless of the error codes that including files may use.

The LOG_POST_* macros just write a string to the log file, and are useful if a human-readable log file is desired. The output from the ERR_POST_* macros is not easily read by humans, but facilitates automatic indexing for searching and/or error statistics. There are multiple flags to control the appearance of the message generated by the ERR_POST_* macros.

The LOG_POST_* and ERR_POST_* macros implicitly create a temporary CNcbiDiag object and put the passed “message” into it with a default severity of Error. A severity level manipulator can be applied if desired, to modify the message’s severity level. For example:

long lll = 345;
ERR_POST_X(1, "My ERR_POST message, print long: " << lll);

would write to the diagnostic stream something like:

Error: (1501.1) My ERR_POST message, print long: 345


double ddd = 123.345;
ERR_POST_X(1, Warning << "My ERR_POST message, print double: " << ddd);

would write to the diagnostic stream something like:

Warning: (1501.1) My ERR_POST message, print double: 123.345

See the Log File Format section for more information on controlling the format of diagnostics messages.

Note: Most of the above macros make use of the macro definition NCBI_USE_ERRCODE_X. This definition must be present in your source code, and must be defined in terms of an existing error code name. By convention, error code names are defined in header file named error_codes.hpp in the relevant directory, for example include/corelib/error_codes.hpp.

To set up new error codes, pick appropriate names and error code numbers that don’t match existing values, and decide how many subcodes you’ll need for each error code. For example, the following sets up three error codes to deal with different categories of errors within a library, and specifies the number of subcodes for each category:

// Note: The following should be in src/app/my_prog/error_codes.hpp.
NCBI_DEFINE_ERRCODE_X(MyLib_Cat1, 1501, 5);
NCBI_DEFINE_ERRCODE_X(MyLib_Cat2, 1502, 6);
NCBI_DEFINE_ERRCODE_X(MyLib_Cat3, 1503, 1);
// where:
//      MyLib_*   -- the error code names
//      1501, etc -- the error code numbers, typically starting at N*100+1
//      5, etc    -- how many subcodes you need for the given error code

Now you can use the error code in your library’s implementation:

// The following should be in your source files.
// include the relevant error_codes header, for example:
#include <include/corelib/error_codes.hpp>
#define NCBI_USE_ERRCODE_X   MyLib_Cat1 // sets the default error code for this file
    ERR_POST_X(5, Critical << "Your message here."); // uses the default error code

Generally, the default error code and the ERR_POST_X macro should be used. If it is necessary to use a non-default error code, that error code and the appropriate subcode may be used with the ErrCode manipulator in the ERR_POST macro. For example:

// use a non-default error code (1501 in this example) and subcode 3
ERR_POST(ErrCode(1501, 3) << "My error message.");

The _TRACE macro

The _TRACE(message) macro is a debugging tool that allows the user to insert trace statements that will only be posted if the code was compiled in debug mode, and provided that the tracing has been turned on. If DIAG_TRACE is defined as an environment variable, or as an entry in the [DEBUG] section of your configuration file (*.ini), the initial state of tracing is on. By default, if no such variable or registry entry is defined, tracing is off. SetDiagTrace (EDiagTrace enable, EDiagTrace default) is used to turn tracing on/off.

Just like ERR_POST, the _TRACE macro takes a message, and the message will be posted only if tracing has been enabled. For example:

_TRACE("Testing the _TRACE macro");
_TRACE("Testing the _TRACE macro AGAIN");

Here, only the second trace message will be posted, as tracing is disabled when the first _TRACE() macro call is executed.

Performance Logging

The C++ Toolkit includes a performance logging API that is independent of the general diagnostics API. This allows independent control, analysis, and management of the performance data. Performance log files are created just like other log files, except that the extension is .perf instead of .log, for example. Performance data can be found in AppLog by searching for the “perf” event (see the events and messages section for more details about events).

The performance logging classes and macros are:

  • CPerfLogGuard

    • The CPerfLogGuard class will generally be the first choice for performance logging. If you want to use a PERF_POST* macro, then use CPerfLogger to create the logger object.

    • CPerfLogGuard measures elapsed time and posts a one-line entry in the performance log.

    • CPerfLogGuard should be used for measuring just one operation.

    • Extra parameters can be added using AddParameter().

    • You can call Start() and Suspend() as many times as you want after creating the logger and before posting or discarding.

    • End measurement with Post() or Discard(). If one of these isn’t called before the logger is destroyed, the destructor will post a log entry with a status code of 500.

    • CPerfLogGuard has built-in integrity checks to ensure that only one Post() or Discard() call is made, Suspend() isn’t called when the time isn’t running, etc.

  • CPerfLogger

    • The CPerfLogger class can be used on its own, but it’s best to only use it if you need to create a logger for use in a PERF_POST* macro. CPerfLogger is slightly lower-level than CPerfLogGuard but is otherwise very similar, except that CPerfLogGuard offers generally desirable guard features.

    • Note: If you use CPerfLogger on its own, and logging is off, then neither logging nor timing will be done. However, the extra record will be put into the log if the following construct is used:


      Therefore, it’s best to avoid that construct and use the CPerfLogGuard class or a PERF_POST macro instead.


    • Use the PERF_POST macro if you find it more convenient than CPerfLogGuard, or if you’d like to possibly save a few CPU cycles when performance logging is globally turned off.

    • Use the PERF_POST_DB macro for the same reasons as the PERF_POST macro, but specifically when working with a database.

Performance logging is turned off by default, but can be globally turned on using the environment variable LOG_PerfLogging or the registry:

PerfLogging = true

It can also be turned on or off at runtime by calling CPerfLogger::SetON().

Here is a typical usage example:

CPerfLogGuard perf("unique task description");
// do something to be timed
perf.Post(200, "finished");

This example shows nested logging:

void some_func(void)
    CPerfLogGuard perf_overall("instrument an entire function");

    CPerfLogGuard perf_init("init");
    // initialization code to be timed ...
        200,                // status code
        "init finished");   // status description string

    CPerfLogGuard perf_loop("loop");
    for (int i=0; i<10; ++i) {
        CPerfLogGuard perf_task1("task1");
        // sub-task 1 ...
        perf_task1.Post(200); // the status description string is optional

        if (true) {
            CPerfLogGuard perf_cond("conditional");
            perf_cond.AddParameter("iter", NStr::NumericToString(i));
            // conditional task ...
            perf_cond.Post(200, "conditional finished");
    perf_loop.Post(200, "loop finished");

    perf_overall.Post(200, "function finished"); 

Stack Traces

CStackTrace objects have special formatting: a “Stack trace:” line is added before the stack trace and standard indentation is used. This formatting is also used when printing the stack trace for exceptions.

Using stack traces with diagnostics is discussed in the following topics:

Printing a Stack Trace

A stack trace can be saved simply by creating a CStackTrace object. Then the object can be posted in an error message, for example:

ERR_POST_X(1, Error << "Your message here." << CStackTrace());

An example of a stack trace output on Linux:

Error: (1501.1) Your message here.
     Stack trace:
      ./my_prog ???:0 ncbi::CStackTraceImpl::CStackTraceImpl() offset=0x5D
      ./my_prog ???:0 ncbi::CStackTrace::CStackTrace(std::string const&) offset=0x28
      ./my_prog ???:0 CMyProg::Run() offset=0xAF3
      ./my_prog ???:0 ncbi::CNcbiApplication::x_TryMain(ncbi::EAppMyProgStream, char const*, int*, bool*) offset=0x6C8
      ./my_prog ???:0 ncbi::CNcbiApplication::AppMain(int, char const* const*, char const* const*, ncbi::EAppMyProgStream, char const*, std::string const&) offset=0x11BA
      ./my_prog ???:0 main offset=0x60
      /lib64/tls/ ???:0 __libc_start_main offset=0xEA
      ./my_prog ???:0 std::__throw_logic_error(char const*) offset=0x62

Obtaining a Stack Trace for Exceptions

The stack trace can be saved by CException and derived classes automatically if the exception’s severity is equal to or above the level set in the EXCEPTION_STACK_TRACE_LEVEL environment variable or configuration parameter. The default level is Critical, so that most exceptions do not save the stack trace (the default exception’s severity is Error).

When printing an exception, the diagnostics code checks if a stack trace is available and if so, automatically prints the stack trace along with the exception.

An example of an exception with a stack trace on Linux:

Error: (106.16) Application's execution failed
NCBI C++ Exception:
    Error: (CMyException::eMyErrorXyz) Your message here.
     Stack trace:
      ./my_prog ???:0 ncbi::CStackTraceImpl::CStackTraceImpl() offset=0x5D
      ./my_prog ???:0 ncbi::CStackTrace::CStackTrace(std::string const&) offset=0x28
      ./my_prog ???:0 ncbi::CException::x_GetStackTrace() offset=0x86
      ./my_prog ???:0 ncbi::CException::x_Init(ncbi::CTestCompileInfo const&, std::string const&, ncbi::CException const*, ncbi::ETestSev) offset=0xE9
      ./my_prog ???:0 ncbi::CException::CException(ncbi::CTestCompileInfo const&, ncbi::CException const*, ncbi::CException::EErrCode, std::string const&, ncbi::ETestSev) offset=0x119
      ./my_prog ???:0 CMyException::CMyException(ncbi::CTestCompileInfo const&, ncbi::CException const*, CMyException::EErrCode, std::string const&, ncbi::ETestSev) offset=0x43
      ./my_prog ???:0 CMyTestTest::Run() offset=0xD3A
      ./my_prog ???:0 ncbi::CNcbiApplication::x_TryMain(ncbi::EAppTestStream, char const*, int*, bool*) offset=0x6C8
      ./my_prog ???:0 ncbi::CNcbiApplication::AppMain(int, char const* const*, char const* const*, ncbi::EAppTestStream, char const*, std::string const&) offset=0x11BA
      ./my_prog ???:0 main offset=0x60
      /lib64/tls/ ???:0 __libc_start_main offset=0xEA
      ./my_prog ???:0 std::__throw_logic_error(char const*) offset=0x62

Logging modules and its configuration parameters

Logging can be done from different modules and sources, written in different languages and having different APIs. Below is a list of each module and description for all its configuration parameters.


Native C++ logging. You can find description of all parameters in the Logging section, Library Configuration chapter.


CLog is a pure C library to provide the C++ Toolkit-like logging semantics and output for C/C++ programs and CGIs.

These parameters tune the usage and behavior of the library and all based on it applications:

Configuration Parameter Purpose Valid value Default
NCBI_LOG_HIT_ID Defines the default hit ID, which is used for application and for any request which has no explicit hit ID set. any valid PHID string ””
HTTP_NCBI_PHID Same as NCBI_LOG_HIT_ID, but passed through HTTP headers. Have a priority over NCBI_LOG_HIT_ID. any valid PHID string ””
NCBI_LOG_SESSION_ID Defines the default session ID, which is used for any request which has no explicit session ID set. any valid session ID string “UNK_SESSION”
HTTP_NCBI_SID Same as NCBI_LOG_SESSION_ID, but passed through HTTP headers. Have a priority over NCBI_LOG_SESSION_ID. any valid session ID string “UNK_SESSION”
SERVER_PORT Web server/service port. Specifies one of the possible locations to store logging files for CGI, see Where Diagnostic Messages Go. a positive integer (none)
NCBI_CONFIG__LOG__FILE Reset the log file to the specified file. By default, if NcbiLog_SetDestination() is not called or set to eNcbiLog_Default, and environment variable $NCBI_CONFIG__LOG__FILE points to some location on a file system, its value will be used as base name for logging. Also, it can have special value “-“ to redirect all output to STDERR. Note, this is not a preferred way to set logging to a local file, this exists for a backward compatibility only. Please use NcbiLog_SetDestination(eNcbiLog_File) instead. a valid file name, or “-“ (none)
NCBI_CLOG_REPORT_ERRORS Report critical errors to stderr if defined to positive values. If CLog destination is set to stderr as well, do nothing. “Y”, “y”, “1” (none)
LOG_ISSUED_SUBHIT_LIMIT Specify the maximum number of sub-PHIDs that can be reported to the AppLog by a single request. unsigned integer 200


To allow logging from scripts we have a command-line utility — ncbi_applog. It is based on CLog library, so it accepts all parameters specified for that library, and also some extra:

Configuration Parameter Purpose Valid value Default
NCBI_APPLOG_TOKEN Utility returns tokens for start_app, start_request and stop_request commands, that should be used as mandatory argument for all subsequent calls. It is possible to save returned value to NCBI_APPLOG_TOKEN environment variable and pass empty string “” instead of the real token argument.   (none)
NCBI_APPLOG_SITE Value for logsite parameter. If logsite is specified, that the application name in the passed logging data will be replaced with logsite value and original application name have added as ‘extra’ record to logs. -logsite command line argument have a priority over environment variable. Also, logsite is used for checking “/log/” location for writing logs. If logsite is not specified and local logging is impossible, all logging going through CGI redirects, that automatically assign “dev” logsite, if it is not specified.   (none) for local logging,
“dev” for CGI

NcbiApplogCGI = http://...
Logging CGI, automatically used if /log is not accessible or writable on a current machine. Could be used to change hardcoded value, although it is not recommended. a valid URL (none)

NcbiApplogDestination = ...
Set logging destnation. If this parameter is specified and not ‘default’, it disable CGI redirecting. See Where Diagnostic Messages Go. default, cwd, stdlog, stdout, stderr, file default (stdlog)

NcbiApplogDestinationFile = <path_to_logfile>
If the output destination is set to “file”, this parameter will define a base name for a log file. If splitting is disabled, there will be a single .log file, or several files with .err/.perf/.trace extentions otherwise.. a valid file name (with path or not) (none)
NCBI_CONFIG__LOG__FILE Same as for CLog, but also disable CGI-redirecting. All logging will be done locally, to the provided in this variable base name for logging files or to standard error for special value “-“. If for some reason specified location is non-writable, you will have an error. This environment variable have a higher priority than the output destination in NCBI_CONFIG__NCBIAPPLOG_DESTINATION. Note, this is not a preferred way to set logging to a local file, this exists for a backward compatibility only. Please use NCBI_CONFIG__NCBIAPPLOG_DESTINATION set to “file” instead. a valid file name, or “-“ (none)

Below is an example how to use it. Please note that this example is very simplified and present for illustration purposes only. You can find real working wrapper script that allow to run an arbitrary application and report its calls to AppLog here.

# Wrapper script for an arbitrary application to report its calls to AppLog.
# NOTE 1: We use simple command lines and limited set of arguments.
#         You can get full list of arguments and its description using:
#         /opt/ncbi/bin/ncbi_applog-1 [command] -help.
# NOTE 2: Each key/value in the parameters pairs for -param argument shoould be
#         URL-encoded. We don't doing it here for illustration purposes.
# NOTE 3: It is recommended to check exit codes for each ncbi_applog call.

# Path to ncbi_applog utility

# Path to your application, and it's name as it will be shown in AppLog

# For debugging purposes uncomment 2 lines below. This will redirect
# all output to the current directory instead of sending it to AppLog.
# See files named 'my_app_name.*'.


# Log starting, specifying application name and pid for our wrapping script.
# Getting token needed for all subsequent calls.

app_token=`$APPLOG start_app -appname "$app_name" -pid "$$"`

# Start a request. You can run an application multiple times between
# "start_app" and "stop_app" commands, each time with its own parameters.
# You can use single request or wrap each run to its own request,
# but it is recommended to have at least one.
# Each request have its own token, needed to distinquish it from all other
# requests, and it should be used for all request-specific calls.

req_token=`$APPLOG start_request "$app_token" -param "user=${USER}&pwd=${PWD}&${extra_params}"`

# Execute an application

"$app_executable" "$@"

# To log exit code correctly for AppLog, it is recommended to translate
# application's exit code to HTTP-like status code, where 200 mean OK (no error).

case $app_exit in
    0 ) log_app_exit=200 ;;
  200 ) log_app_exit=199 ;;
    * ) log_app_exit=$app_exit ;;

# Log stopping state for our request and application,

$APPLOG stop_request "$req_token" -status $log_app_exit
$APPLOG stop_app     "$app_token" -status $log_app_exit

exit $app_exit